Last updated on 2026-09-08 09:53:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.71 | 226.94 | 230.65 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.66 | 212.91 | 215.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.65 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 184.77 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 135.00 | 140.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.92 | 207.03 | 210.95 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.44 | 203.68 | 207.12 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 6.00 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 33.00 | 34.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 157.00 | 164.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-07 02:13:22.942 R[63293:98549] 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, 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)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
4: ComputeError(predictions$Observations, predictions$Predictions)
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
Traceback:
1: RowCumsum(valid) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
17:
2: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
doTryCatch(return(expr), name, parentenv, handler)
18: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
19: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, tryCatchList(expr, classes, parentenv, handlers)
20: 9:
Traceback:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatchOne(expr, names, parentenv, handlers[[1L]]) 1: mc.preschedule = TRUE), error = function(e) NULL)
RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
10: ignoreNan = ignoreNan, backend = backend)21:
4: ComputeError(predictions$Observations, predictions$Predictions)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)tryCatchList(expr, classes, parentenv, handlers) 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,
11: tieBreak = FALSE, verbose = verbose)24: tryCatch(expr, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
call <- conditionCall(e) if (!is.null(call)) { 6: ignoreNan = ignoreNan, backend = backend)
4: FUN(X[[i]], ...)eval(expr, envir) if (identical(call[[1L]], quote(doTryCatch)))
7: lapply(X = S, FUN = FUN, ...)
8:
ComputeError(predictions$Observations, predictions$Predictions)
call <- sys.call(-4L)doTryCatch(return(expr), name, parentenv, handler)25: eval(expr, envir)
dcall <- deparse(call, nlines = 1L) 5:
26: withVisible(eval(expr, envir))
27: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatch(expr, error = function(e) { prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]withCallingHandlers(code, error = function (e) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")rlang::entrace(e), message = function (cnd) if (is.na(w)) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- conditionCall(e) if (!is.null(call)) { embedded = embedded, validLib = validLib, noTime = noTime, } if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) if (on_message$silence) { ignoreNan = ignoreNan, backend = backend)$predictions) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...) dcall <- deparse(call, nlines = 1L) else prefix <- "Error : "
prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers) msg <- paste0(prefix, conditionMessage(e), "\n") invokeRestart("muffleMessage")
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (is.na(w)) if (!is.null(call)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(seterrmessage(msg[1L])) if (identical(call[[1L]], quote(doTryCatch))) type = "b") call <- sys.call(-4L) }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() if (!silent && isTRUE(getOption("show.error.messages"))) { if (w > LONG) prefix <- paste0(prefix, "\n ") } cat(msg, file = outFile) 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") } .Internal(printDeferredWarnings()) watcher$capture_plot_and_output() } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
if (on_warning$capture) { else prefix <- "Error : "14: if (is.na(w)) msg <- paste0(prefix, conditionMessage(e), "\n") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(seterrmessage(msg[1L]))FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: cnd <- sanitize_call(cnd)doTryCatch(return(expr), name, parentenv, handler)
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)18: type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")})tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
else prefix <- "Error : "28: msg <- paste0(prefix, conditionMessage(e), "\n")eval(call) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)29: eval(call)
.Internal(printDeferredWarnings())19: } invisible(structure(msg, class = "try-error", condition = e))})
12: cat(msg, file = outFile)tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
20:
12: 13: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)14: 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
FUN(X[[i]], ...)
watcher$print_value(ev$value, ev$visible, envir)15: lapply(seq_len(cores), inner.do) } TRUE}, handlers)
15: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18:
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: lapply(seq_len(cores), inner.do)doWithOneRestart(return(expr), restart)21:
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
tryCatchOne(expr, names, parentenv, handlers[[1L]]) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
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)38:
19: tryCatchList(expr, classes, parentenv, handlers)evaluate::evaluate(...)
24:
19: eval(expr, envir)
25: eval(expr, envir)tryCatchList(expr, classes, parentenv, handlers)20:
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 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)
39: 25:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(expr, envir)
26: withVisible(eval(expr, envir))
27: 20: 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$render, options))withCallingHandlers(code, error = function (e) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output(){
watcher$capture_plot_and_output() if (on_message$capture) { if (on_message$capture) { mc.preschedule = TRUE), error = function(e) NULL)40: in_dir(input_dir(), expr) watcher$push(cnd) watcher$push(cnd) } } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) {
21: SweepApply(theta, worker, numProcess)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) {22: unlist(SweepApply(theta, worker, numProcess)) return()
stop_on_error = if (is.numeric(options$error)) options$error else {23: }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (options$error && options$include) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 0L if (on_warning$silence) { else 2L }, output_handler = knit_handlers(options$render, options)))
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)})42:
28: E = E, showPlot = TRUE)eval(call)eng_r(options)
43:
}block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { watcher$capture_plot_and_output()
24: eval(expr, envir)
25: if (progress && is.function(pb$interrupt)) 29: eval(expr, envir)eval(call) pb$interrupt() if (on_warning$capture) { 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()
26: withVisible(eval(expr, envir)) 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$interrupt)) cnd <- sanitize_call(cnd) pb$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))
watcher$push(cnd)27: } if (on_warning$silence) {
30: with_handlers({ paste0("\n", rule(), error, "\n", rule())) invokeRestart("muffleWarning") }withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()}, error = function (cnd) { if (on_message$capture) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
watcher$push(cnd) cnd <- sanitize_call(cnd)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: } }engine$weave(file, quiet = quiet, encoding = enc)
54: TRUE watcher$push(cnd)}, handlers)doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_message$silence) { invokeRestart("muffleMessage") switch(on_error, continue = invokeRestart("eval_continue"),
56: tryCatchList(expr, classes, parentenv, handlers)
57: stop = invokeRestart("eval_stop"), error = NULL)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)})31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]]) }
28: }, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (!have.makefile && vignette_is_tex(output)) { return()
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)eval(call) texi2pdf(file = output, clean = FALSE, quiet = quiet)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) } output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }
outputs <- c(outputs, output)29: eval(call)
}, error = function(e) { thisOK <<- FALSE watcher$capture_plot_and_output()
36: withRestartList(expr, restarts)
fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE37: }, handlers)
31:
if (on_warning$capture) {doWithOneRestart(return(expr), restart)
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/Rtmp2mKQrE/filecd1b42f6a2c2.rds")
An irrecoverable exception occurred. R is aborting now ...
withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)32: cnd <- sanitize_call(cnd)withOneRestart(expr, restarts[[1L]]) }
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: watcher$push(cnd)withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { } if (on_warning$silence) { invokeRestart("muffleWarning") } TRUE}, error = function (cnd) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {{ watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
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$render, options)))
42: eng_r(options)
43: watcher$push(cnd) if (options$error && options$include) block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
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) { 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()))
0L else 2L28: eval(call)
29: eval(call)
30: with_handlers({48: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options))
} TRUE}, handlers)
error = function(e) { if (progress && is.function(pb$interrupt)) 31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 40: 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))
34: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: doWithOneRestart(return(expr), restart)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(), in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, output_dir = getwd(), ...)36: keep_message = if (is.numeric(options$message)) TRUE else options$message,
52: 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$visible, envir)vweave_rmarkdown(...)
} TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
40: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))in_dir(input_dir(), expr)53:
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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: engine$weave(file, quiet = quiet, encoding = enc)eng_r(options)
42: 54: doTryCatch(return(expr), name, parentenv, handler)
55:
43: block_exec(params)
44: call_block(x)
45: eng_r(options)tryCatchOne(expr, names, parentenv, handlers[[1L]])
process_group(group)
46: 43: block_exec(params)
44: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call_block(x) error = function(e) {56: if (progress && is.function(pb$interrupt))
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 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: tryCatchList(expr, classes, parentenv, handlers)engine$weave(file, quiet = quiet, encoding = enc)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) engine = engine) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)54:
49: process_file(text, output)
doTryCatch(return(expr), name, parentenv, handler)
55: 50: tryCatchOne(expr, names, parentenv, handlers[[1L]])
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
56: 51: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSErmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) } 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/Rtmp2mKQrE/filecd1b42f6a2c2.rds")
An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler) outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
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/Rtmp2mKQrE/filecd1b42f6a2c2.rds")
An irrecoverable exception occurred. R is aborting now ...
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/Rtmp2mKQrE/filecd1b42f6a2c2.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