Last updated on 2026-08-16 08:50:42 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 | 2.11 | 237.63 | 239.74 | 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 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 44.00 | 45.00 | 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
2026-08-16 16:39:00.952 R[42679:61918] 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: eval(expr, envir)
25: eval(expr, envir)
26: 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$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, 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)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 32: withOneRestart(expr, restarts[[1L]])
33: 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, 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({ ignoreNan = ignoreNan, backend = backend)$predictions)
Traceback:
1: 6: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }FUN(X[[i]], ...) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
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$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 7: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 38: embedded = embedded, validLib = validLib, noTime = noTime, evaluate::evaluate(...)lapply(X = S, FUN = FUN, ...)
ignoreNan = ignoreNan, backend = backend)$predictions)
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$error else { 8: if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 0L10: tryCatchList(expr, classes, parentenv, handlers) else 2L
Traceback:
tryCatchList(expr, classes, parentenv, handlers) 1: 11: }, output_handler = knit_handlers(options$render, options)))tryCatch(expr, error = function(e) {
11: RowCumsum(valid)tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch)))
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, ": ")42: LONG <- 75L 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, sm <- strsplit(conditionMessage(e), "\n")[[1L]] tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- sys.call(-4L)eng_r(options) embedded = embedded, validLib = validLib, noTime = noTime, dcall <- deparse(call, nlines = 1L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste("Error in", dcall, ": ") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], LONG <- 75L ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions) type = "b")
43: 5: block_exec(params)
44: call_block(x) if (w > LONG) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, prefix <- paste0(prefix, "\n ") sm <- strsplit(conditionMessage(e), "\n")[[1L]] knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
45: process_group(group)
46: embedded = embedded, validLib = validLib, noTime = noTime, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ignoreNan = ignoreNan, backend = backend)$predictions) error = function(e) {
}) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
if (progress && is.function(pb$interrupt)) 14: FUN(X[[i]], ...) pb$interrupt()
if (is.na(w)) if (is_R_CMD_build() || is_R_CMD_check()) 15: error <<- format(e) })
47: 6: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {FUN(X[[i]], ...) error = function(e) { cat(msg, file = outFile) if (progress && is.function(pb$interrupt)) pb$interrupt() .Internal(printDeferredWarnings())
lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
if (is_R_CMD_build() || is_R_CMD_check()) } 7: invisible(structure(msg, class = "try-error", condition = e))})
17: 12: error <<- format(e)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)lapply(X = S, FUN = FUN, ...)
}), list(rlang_trace_top_env = knit_global()))
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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() 8:
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)13: }), list(rlang_trace_top_env = knit_global())), function(loc) {doTryCatch(return(expr), name, parentenv, handler)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) setwd(wd)
write_utf8(res, output %n% stdout())
19: paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)14: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
10: tryCatchList(expr, classes, parentenv, handlers)
15:
49: lapply(seq_len(cores), inner.do)11: 20: 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:
tryCatch(expr, error = function(e) {vweave_rmarkdown(...)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 53: call <- conditionCall(e)16: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) call <- sys.call(-4L) mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
engine$weave(file, quiet = quiet, encoding = enc)
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 19: E = E, showPlot = TRUE) dcall <- deparse(call, nlines = 1L)tryCatchList(expr, classes, parentenv, handlers)
20: 54: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: 24: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
prefix <- paste("Error in", dcall, ": ")24: LONG <- 75LdoTryCatch(return(expr), name, parentenv, handler)eval(expr, envir)eval(expr, envir)
25: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w))
25: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) eval(expr, envir)eval(expr, envir)
prefix <- paste0(prefix, "\n ")
}26: else prefix <- "Error : "26: 55: withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: msg <- paste0(prefix, conditionMessage(e), "\n")withVisible(eval(expr, envir))
.Internal(seterrmessage(msg[1L]))tryCatchList(expr, classes, parentenv, handlers)27: if (!silent && isTRUE(getOption("show.error.messages"))) {
27: withCallingHandlers(code, error = function (e) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()}) if (on_message$capture) {withCallingHandlers(code, error = function (e)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
rlang::entrace(e), message = function (cnd) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)13: watcher$push(cnd) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)
14: FUN(X[[i]], ...) } if (on_message$silence) { } 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))) invokeRestart("muffleMessage")
15: {})
watcher$capture_plot_and_output()lapply(seq_len(cores), inner.do) if (on_message$capture) { } watcher$push(cnd)
}16: }, warning = function (cnd) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE){ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$silence) { return() invokeRestart("muffleMessage") }}, warning = function (cnd) 58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 17: { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3ovGdl/file69b775f109c3.rds") }
An irrecoverable exception occurred. R is aborting now ...
watcher$capture_plot_and_output() if (on_warning$capture) {doTryCatch(return(expr), name, parentenv, handler) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)
cnd <- sanitize_call(cnd)18: } watcher$push(cnd) } if (on_warning$silence) { if (on_warning$silence) { invokeRestart("muffleWarning") }tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function (cnd) invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output(){ cnd <- sanitize_call(cnd)
19: tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
stop = invokeRestart("eval_stop"), error = NULL)29: })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))28:
eval(call)
29: eval(call)
30: eval(call)23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
with_handlers({30: with_handlers({ for (expr in tle$exprs) { for (expr in tle$exprs) {25: eval(expr, envir)
26: 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$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) ev <- withVisible(eval(expr, envir)) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]){ if (getOption("warn") >= 2 || getOption("warn") < 0) {
34: doWithOneRestart(return(expr), restart)31: doWithOneRestart(return(expr), restart)
32: 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$exprs) {35: ev <- withVisible(eval(expr, envir)) return() } watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, error = function (cnd)
36: 38: withRestartList(expr, restarts)
evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, { watcher$capture_plot_and_output()37: cnd <- sanitize_call(cnd)withRestarts(with_handlers({ for (expr in tle$exprs) { watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() keep_message = if (is.numeric(options$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))
watcher$print_value(ev$value, ev$visible, envir) } TRUE28: eval(call)
29: eval(call)
30: with_handlers({40: for (expr in tle$exprs) {in_dir(input_dir(), expr)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()41: watcher$print_value(ev$value, ev$visible, envir) }38: TRUE}, handlers)
evaluate::evaluate(...)
31: doWithOneRestart(return(expr), restart)39: in_input_dir(evaluate(code, envir = env, new_device = FALSE, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: withOneRestart(expr, restarts[[1L]])
42: 33: eng_r(options)withRestartList(expr, restarts[-nr])
if (options$error && options$include) 0L43: else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: block_exec(params)
44: call_block(x)
34: doWithOneRestart(return(expr), restart)
35: 45: 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) 0LwithOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) {process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { else 2L }, output_handler = knit_handlers(options$render, options)))
if (progress && is.function(pb$interrupt)) 42: eng_r(options)
43: ev <- withVisible(eval(expr, envir))block_exec(params)
pb$interrupt()44: call_block(x) 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()) watcher$capture_plot_and_output() error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error))
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$print_value(ev$value, ev$visible, envir) } error = function(e) { TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) paste0("\n", rule(), error, "\n", rule())) if (progress && is.function(pb$interrupt)) pb$interrupt()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)49: process_file(text, output)
38: evaluate::evaluate(...)
39: })50:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
keep_message = if (is.numeric(options$message)) TRUE else options$message, if (progress && is.function(pb$interrupt)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L pb$interrupt()51: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) else 2L paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }, output_handler = knit_handlers(options$render, options))52: vweave_rmarkdown(...)
40: in_dir(input_dir(), expr)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: process_file(text, output)
56: tryCatchList(expr, classes, parentenv, handlers)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
57: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: tryCatch({vweave_rmarkdown(...)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 {53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
if (options$error && options$include) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
engine$weave(file, quiet = quiet, encoding = enc) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) setwd(startdir)57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
43: 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 = "weave", engine = engine) 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", block_exec(params) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3ovGdl/file69b775f109c3.rds")
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)44: An irrecoverable exception occurred. R is aborting now ...
call_block(x)
45: process_group(group)
46: output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), outputs <- c(outputs, output)}, error = function(e) { 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() 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/Rtmp3ovGdl/file69b775f109c3.rds")
An irrecoverable exception occurred. R is aborting now ...
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/Rtmp3ovGdl/file69b775f109c3.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