Last updated on 2026-08-17 09:49:19 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 | 1.00 | 39.00 | 40.00 | 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
2026-08-17 15:47:14.040 R[40533:59067] 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:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$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) 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)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9:
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)ComputeError(predictions$Observations, predictions$Predictions)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, if (w > LONG) prefix <- paste0(prefix, "\n ") ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))})
12: 4: ComputeError(predictions$Observations, predictions$Predictions)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
8:
doTryCatch(return(expr), name, parentenv, handler)15:
lapply(seq_len(cores), inner.do) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16:
6: FUN(X[[i]], ...)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler) 7: lapply(X = S, FUN = FUN, ...)
10: tryCatchList(expr, classes, parentenv, handlers) 8:
doTryCatch(return(expr), name, parentenv, handler)11:
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(expr, error = function(e) {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: call <- conditionCall(e) if (!is.null(call)) { 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)tryCatch(expr, error = function(e) {
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") call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) if (is.na(w)) dcall <- deparse(call, nlines = 1L)26: withVisible(eval(expr, envir))
27: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } prefix <- paste("Error in", dcall, ": ") prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (on_message$silence) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " if (on_warning$capture) { cnd <- sanitize_call(cnd) .Internal(seterrmessage(msg[1L])) msg <- paste0(prefix, conditionMessage(e), "\n") watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") .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))})
if (!silent && isTRUE(getOption("show.error.messages"))) {}, error = function (cnd) 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: { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: cat(msg, file = outFile)SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", with_handlers({ target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: for (expr in tle$exprs) { .Internal(printDeferredWarnings()) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } }
31: doWithOneRestart(return(expr), restart)
32: invisible(structure(msg, class = "try-error", condition = e)) if (on_message$silence) {withOneRestart(expr, restarts[[1L]])}) invokeRestart("muffleMessage") }}, warning = function (cnd)
{12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
Traceback:
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
if (getOption("warn") >= 2 || getOption("warn") < 0) {14: FUN(X[[i]], ...)
return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)15: watcher$push(cnd)lapply(seq_len(cores), inner.do)
} if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) {33: 1: RowCumsum(valid)
withRestartList(expr, restarts[-nr]) 2: watcher$capture_plot_and_output()
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, cnd <- sanitize_call(cnd) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$push(cnd)
verbose = verbose)34: 17: doTryCatch(return(expr), name, parentenv, handler)
18: doWithOneRestart(return(expr), restart)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19:
tryCatchList(expr, classes, parentenv, handlers)
20: 36: switch(on_error, continue = invokeRestart("eval_continue"), 3: stop = invokeRestart("eval_stop"), error = NULL)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, withRestartList(expr, restarts) mc.preschedule = TRUE), error = function(e) NULL)})
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 28: 37: eval(call)
29: eval(call)
withRestarts(with_handlers({ ignoreNan = ignoreNan, backend = backend)
4: 21: SweepApply(theta, worker, numProcess)
for (expr in tle$exprs) {22: unlist(SweepApply(theta, worker, numProcess))
ComputeError(predictions$Observations, predictions$Predictions)23: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)30: }with_handlers({ TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
39: 32:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
5: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withOneRestart(expr, restarts[[1L]])
33: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, withRestartList(expr, restarts[-nr])25: if (options$error && options$include) eval(expr, envir)
26: withVisible(eval(expr, envir))
27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 0L else 2L }, output_handler = knit_handlers(options$render, options))34: {doWithOneRestart(return(expr), restart) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
watcher$capture_plot_and_output()36: ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: if (on_message$capture) {lapply(X = S, FUN = FUN, ...)
watcher$push(cnd)
}40: withRestartList(expr, restarts)in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: if (on_message$silence) {eng_r(options)
43: invokeRestart("muffleMessage")block_exec(params)
44: 8: call_block(x)
45:
37: withRestarts(with_handlers({ for (expr in tle$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: 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$render, options)) }process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
doTryCatch(return(expr), name, parentenv, handler)}, warning = function (cnd)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: {47:
tryCatchList(expr, classes, parentenv, handlers)40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) {in_dir(input_dir(), expr)
41: cnd <- sanitize_call(cnd)11: in_input_dir(evaluate(code, envir = env, new_device = FALSE, error = function(e) {tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, else prefix <- "Error : " stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd) } if (on_warning$silence) {
if (options$error && options$include) 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() invokeRestart("muffleWarning") } msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) if (is_R_CMD_build() || is_R_CMD_check()) }, error = function (cnd) } invisible(structure(msg, class = "try-error", condition = e)){ watcher$capture_plot_and_output() error <<- format(e) 0L}) cnd <- sanitize_call(cnd) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)49:
15: lapply(seq_len(cores), inner.do)})process_file(text, output) else 2L
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler) }, output_handler = knit_handlers(options$render, options)))
42: 55: 16:
eng_r(options)28:
43: block_exec(params)
44: call_block(x)
45: process_group(group)tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)46:
56: 17: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 29:
error = function(e) {18: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)eval(call)tryCatchList(expr, classes, parentenv, handlers)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
57:
})
19: 47: tryCatchList(expr, classes, parentenv, handlers)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {20: if (progress && is.function(pb$interrupt)) 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) pb$interrupt() }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) TRUEtryCatch({ }), list(rlang_trace_top_env = knit_global()))}, handlers)
mc.preschedule = TRUE), error = function(e) NULL) engine$weave(file, quiet = quiet, encoding = enc)
21: 31: doWithOneRestart(return(expr), restart)
32: SweepApply(theta, worker, numProcess)withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: 48: setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { } if (progress && is.function(pb$interrupt)) 22: pb$interrupt()unlist(SweepApply(theta, worker, numProcess)) if (is_R_CMD_build() || is_R_CMD_check())
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)
error <<- format(e) outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)26:
38: }), list(rlang_trace_top_env = knit_global())), function(loc) {evaluate::evaluate(...) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", setwd(wd) file, conditionMessage(e)))
write_utf8(res, output %n% stdout())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$render, options))
40: in_dir(input_dir(), expr)withVisible(eval(expr, envir)) paste0("\nQuitting from ", loc, if (!is.null(error)) })
58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpztzmkB/file6b5f17a94bf2.rds")41: 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: {
An irrecoverable exception occurred. R is aborting now ...
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
if (getOption("warn") >= 2 || getOption("warn") < 0) {vweave_rmarkdown(...)42: eng_r(options)
53: return() } watcher$capture_plot_and_output()43: block_exec(params)
44: call_block(x) if (on_warning$capture) {engine$weave(file, quiet = quiet, encoding = enc) cnd <- sanitize_call(cnd)
watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }45: process_group(group)}, error = function (cnd)
{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)46: })
54: doTryCatch(return(expr), name, parentenv, handler)
28: eval(call)
55: 29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output <- find_vignette_product(name, by = "texi2pdf", error = function(e) { if (progress && is.function(pb$interrupt)) engine = engine) }eval(call)
outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpztzmkB/file6b5f17a94bf2.rds")
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE pb$interrupt()}, handlers)An irrecoverable exception occurred. R is aborting now ...
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]]) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47:
33: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) 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) {
43: block_exec(params)
44: call_block(x)
45: process_group(group) thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpztzmkB/file6b5f17a94bf2.rds")
An irrecoverable exception occurred. R is aborting now ...
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpztzmkB/file6b5f17a94bf2.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