Last updated on 2026-11-01 07:50:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.71 | 227.73 | 231.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.30 | 242.02 | 244.32 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.82 | 207.25 | 211.07 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.79 | 206.57 | 209.36 | 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 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 40.00 | 42.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 159.00 | 165.00 | 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
2026-11-01 16:37:22.632 R[47769:71707] 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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 ") } 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() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
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: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 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(),
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, output_dir = getwd(), ...) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
52: 6: FUN(X[[i]], ...)vweave_rmarkdown(...)
7: lapply(X = S, FUN = FUN, ...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
9: 56: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
57:
tryCatch({10: engine$weave(file, quiet = quiet, encoding = enc)tryCatchList(expr, classes, parentenv, handlers) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
Traceback:
if (!have.makefile && vignette_is_tex(output)) {11: texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 1: tryCatch(expr, error = function(e) {RowCumsum(valid)
engine = engine) call <- conditionCall(e) 2: } outputs <- c(outputs, output)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, }, error = function(e) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, thisOK <<- FALSE tieBreak = FALSE, verbose = verbose) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) 3: })
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 58: tau = tau, theta = th, exclusionRadius = exclusionRadius, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppoYI7f/file97b3c8cff35.rds") embedded = embedded, validLib = validLib, noTime = noTime, if (!is.null(call)) {
An irrecoverable exception occurred. R is aborting now ...
ignoreNan = ignoreNan, backend = backend)
if (identical(call[[1L]], quote(doTryCatch))) 4: ComputeError(predictions$Observations, predictions$Predictions)
5: call <- sys.call(-4L)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, dcall <- deparse(call, nlines = 1L) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste("Error in", dcall, ": ") embedded = embedded, validLib = validLib, noTime = noTime, LONG <- 75L ignoreNan = ignoreNan, backend = backend)$predictions)
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is.na(w))
10: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchList(expr, classes, parentenv, handlers) type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")11: tryCatch(expr, error = function(e) { call <- conditionCall(e) .Internal(seterrmessage(msg[1L])) if (!is.null(call)) { if (!silent && isTRUE(getOption("show.error.messages"))) { if (identical(call[[1L]], quote(doTryCatch))) cat(msg, file = outFile) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
Traceback:
12: 1: prefix <- paste("Error in", dcall, ": ")RowCumsum(valid)
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")try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: .Internal(seterrmessage(msg[1L]))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (!silent && isTRUE(getOption("show.error.messages"))) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, cat(msg, file = outFile) tieBreak = FALSE, verbose = verbose) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
15: 3:
lapply(seq_len(cores), inner.do)
14: FUN(X[[i]], ...)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
15:
lapply(seq_len(cores), inner.do)17:
doTryCatch(return(expr), name, parentenv, handler)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)18: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)17:
tau = tau, theta = th, exclusionRadius = exclusionRadius, 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", doTryCatch(return(expr), name, parentenv, handler) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: 18: eval(expr, envir)
tryCatchOne(expr, names, parentenv, handlers[[1L]])25:
eval(expr, envir)19: tryCatchList(expr, classes, parentenv, handlers)
26:
withVisible(eval(expr, envir))20:
27: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
mc.preschedule = TRUE), error = function(e) NULL)withCallingHandlers(code, error = function (e) 4:
21: SweepApply(theta, worker, numProcess)
ComputeError(predictions$Observations, predictions$Predictions)22: unlist(SweepApply(theta, worker, numProcess))
23: rlang::entrace(e), message = function (cnd) {
5: watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, } target = "Thrips_imaginis", lib = "1 73", pred = "1 73", knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, watcher$capture_plot_and_output() E = E, showPlot = TRUE)
24: if (on_warning$capture) {eval(expr, envir)
cnd <- sanitize_call(cnd)25: watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") } embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)}, error = function (cnd)
{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)eval(expr, envir) 6: watcher$push(cnd)FUN(X[[i]], ...) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL) 7: 26: })withVisible(eval(expr, envir))
lapply(X = S, FUN = FUN, ...)28:
27:
eval(call) 8:
29: doTryCatch(return(expr), name, parentenv, handler)eval(call)
withCallingHandlers(code, error = function (e) 30: with_handlers({ for (expr in tle$exprs) {rlang::entrace(e), message = function (cnd) 9: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
}{ TRUE10: }, handlers) watcher$capture_plot_and_output()
31: doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
32:
11: withOneRestart(expr, restarts[[1L]]) if (on_message$capture) { watcher$push(cnd) }
if (on_message$silence) {33: withRestartList(expr, restarts[-nr]) invokeRestart("muffleMessage")
34: tryCatch(expr, error = function(e) {doWithOneRestart(return(expr), restart) call <- conditionCall(e)
if (!is.null(call)) {35: if (identical(call[[1L]], quote(doTryCatch))) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)36: prefix <- paste("Error in", dcall, ": ")withRestartList(expr, restarts) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]
37: withRestarts(with_handlers({ }}, warning = function (cnd) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (getOption("warn") >= 2 || getOption("warn") < 0) { if (is.na(w)) return() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") watcher$capture_plot_and_output() if (on_warning$capture) { if (w > LONG) prefix <- paste0(prefix, "\n ") for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) } watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") TRUE .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) cnd <- sanitize_call(cnd) }
invisible(structure(msg, class = "try-error", condition = e)) watcher$push(cnd)38: evaluate::evaluate(...)
})
39: }12: if (on_warning$silence) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleWarning")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }}, error = function (cnd)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: stop_on_error = if (is.numeric(options$error)) options$error else {FUN(X[[i]], ...)
if (options$error && options$include) 15: lapply(seq_len(cores), inner.do) 0L
else 2L16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler){ 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) }, output_handler = knit_handlers(options$render, options))})
40: in_dir(input_dir(), expr)
41: 28: in_input_dir(evaluate(code, envir = env, new_device = FALSE, eval(call) keep_warning = if (is.numeric(options$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$error else {29: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))eval(call)
30: with_handlers({
for (expr in tle$exprs) {18: ev <- withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()42: watcher$print_value(ev$value, ev$visible, envir)eng_r(options)
}43: TRUEblock_exec(params)
}, handlers)
19:
tryCatchList(expr, classes, parentenv, handlers)
44: 31: 20: call_block(x)doWithOneRestart(return(expr), restart)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
45: mc.preschedule = TRUE), error = function(e) NULL)32: process_group(group)withOneRestart(expr, restarts[[1L]])
46: 33:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {withRestartList(expr, restarts[-nr])21:
if (progress && is.function(pb$interrupt)) 34: SweepApply(theta, worker, numProcess) pb$interrupt()doWithOneRestart(return(expr), restart)
22: if (is_R_CMD_build() || is_R_CMD_check()) 35: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])unlist(SweepApply(theta, worker, numProcess))
})
23: 47: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), target = "Thrips_imaginis", lib = "1 73", pred = "1 73", error = function(e) { if (progress && is.function(pb$interrupt)) 36: pb$interrupt()withRestartList(expr, restarts) E = E, showPlot = TRUE)
if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)24: }), list(rlang_trace_top_env = knit_global()))
eval(expr, envir)48:
37: 25: withRestarts(with_handlers({xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(expr, envir) error = function(e) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) pb$interrupt()
}26: if (is_R_CMD_build() || is_R_CMD_check()) withVisible(eval(expr, envir)) TRUE
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)27: setwd(wd)
38: withCallingHandlers(code, error = function (e) write_utf8(res, output %n% stdout())evaluate::evaluate(...) paste0("\nQuitting from ", loc, if (!is.null(error))
rlang::entrace(e), message = function (cnd) paste0("\n", rule(), error, "\n", rule()))39: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, {49: watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message, process_file(text, output) if (on_message$capture) {
50: watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) } 0L
if (on_message$silence) { else 2L invokeRestart("muffleMessage") }51: }, output_handler = knit_handlers(options$render, options))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
40: output_dir = getwd(), ...)in_dir(input_dir(), expr)}, warning = function (cnd)
{
41: 52: if (getOption("warn") >= 2 || getOption("warn") < 0) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, vweave_rmarkdown(...) return()
} keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 53: watcher$capture_plot_and_output()engine$weave(file, quiet = quiet, encoding = enc) keep_message = if (is.numeric(options$message)) TRUE else options$message,
if (on_warning$capture) { stop_on_error = if (is.numeric(options$error)) options$error else { cnd <- sanitize_call(cnd) watcher$push(cnd)54: if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler) }
if (on_warning$silence) {55: invokeRestart("muffleWarning") 0LtryCatchOne(expr, names, parentenv, handlers[[1L]]) } else 2L
}, error = function (cnd) { }, output_handler = knit_handlers(options$render, options)))
watcher$capture_plot_and_output()42: 56: eng_r(options) cnd <- sanitize_call(cnd)tryCatchList(expr, classes, parentenv, handlers)
43:
watcher$push(cnd)57: switch(on_error, continue = invokeRestart("eval_continue"), block_exec(params) stop = invokeRestart("eval_stop"), error = NULL)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)44: output <- find_vignette_product(name, by = "weave", engine = engine)}) if (!have.makefile && vignette_is_tex(output)) {call_block(x)
texi2pdf(file = output, clean = FALSE, quiet = quiet)
28: output <- find_vignette_product(name, by = "texi2pdf", 45: eval(call) engine = engine)process_group(group)
29: 46: }withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(call) outputs <- c(outputs, output) error = function(e) {
}, error = function(e) { thisOK <<- FALSE30: if (progress && is.function(pb$interrupt)) fails <<- c(fails, file)with_handlers({ pb$interrupt() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", for (expr in tle$exprs) { file, conditionMessage(e))) if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }) }
TRUE47: }, handlers)})
31:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), doWithOneRestart(return(expr), restart)58: error = function(e) { if (progress && is.function(pb$interrupt)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt() skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppoYI7f/file97b3c8cff35.rds")
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)An irrecoverable exception occurred. R is aborting now ...
32: }), list(rlang_trace_top_env = knit_global()))
48: withOneRestart(expr, restarts[[1L]])xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
33: error = function(e) { if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr]) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {34: setwd(wd) write_utf8(res, output %n% stdout())doWithOneRestart(return(expr), restart) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
35: 49: process_file(text, output)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
50: 36: withRestartList(expr, restarts)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
37: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) output_dir = getwd(), ...) watcher$capture_plot_and_output()
52: watcher$print_value(ev$value, ev$visible, envir)vweave_rmarkdown(...) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38:
53: engine$weave(file, quiet = quiet, encoding = enc)evaluate::evaluate(...)
39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {54: if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler) 0L else 2L
}, output_handler = knit_handlers(options$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, 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
0L else 2L56: tryCatchList(expr, classes, parentenv, handlers)
}, output_handler = knit_handlers(options$render, options)))
57: tryCatch({42: engine$weave(file, quiet = quiet, encoding = enc)eng_r(options)
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)43: block_exec(params)
if (!have.makefile && vignette_is_tex(output)) {44: texi2pdf(file = output, clean = FALSE, quiet = quiet)call_block(x)
output <- find_vignette_product(name, by = "texi2pdf", 45: process_group(group) engine = engine)
46: }withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { outputs <- c(outputs, output)}, error = function(e) { if (progress && is.function(pb$interrupt)) thisOK <<- FALSE pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) fails <<- c(fails, file) error <<- format(e) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) })})
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 58: error = function(e) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppoYI7f/file97b3c8cff35.rds") if (progress && is.function(pb$interrupt))
pb$interrupt()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()))
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/RtmppoYI7f/file97b3c8cff35.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