Last updated on 2026-10-29 23:00:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.97 | 226.48 | 230.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.35 | 216.20 | 218.55 | 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 | 3.10 | 211.40 | 214.50 | 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 | 8.00 | 161.00 | 169.00 | 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
2026-10-30 04:17:36.904 R[49713:76850] 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$visible, envir) } TRUE}, handlers)
Traceback:
31: 1: RowCumsum(valid)doWithOneRestart(return(expr), restart)
2: 32: withOneRestart(expr, restarts[[1L]])FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 33: tieBreak = FALSE, verbose = verbose)withRestartList(expr, restarts[-nr])
34: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, doWithOneRestart(return(expr), restart)
tau = tau, theta = th, exclusionRadius = exclusionRadius, 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)36:
4: withRestartList(expr, restarts)ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 37: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, withRestarts(with_handlers({ embedded = embedded, validLib = validLib, noTime = noTime, for (expr in tle$exprs) { ignoreNan = ignoreNan, backend = backend)$predictions)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() 6: watcher$print_value(ev$value, ev$visible, envir)FUN(X[[i]], ...) }
TRUE 7: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)38:
evaluate::evaluate(...)
9: 39: tryCatchOne(expr, names, parentenv, handlers[[1L]])evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
10: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {tryCatchList(expr, classes, parentenv, handlers) if (options$error && options$include)
0L11: else 2L }, output_handler = knit_handlers(options$render, options))tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) {40: if (identical(call[[1L]], quote(doTryCatch))) in_dir(input_dir(), expr) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, prefix <- paste("Error in", dcall, ": ") keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, LONG <- 75L keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (options$error && options$include) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 0L if (is.na(w)) else 2L w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, output_handler = knit_handlers(options$render, options))) type = "b")
if (w > LONG) 42: prefix <- paste0(prefix, "\n ")eng_r(options)
}43: block_exec(params) else prefix <- "Error : "
44: msg <- paste0(prefix, conditionMessage(e), "\n")call_block(x) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {45: cat(msg, file = outFile)process_group(group) .Internal(printDeferredWarnings())
}46: invisible(structure(msg, class = "try-error", condition = e))})withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {12: if (progress && is.function(pb$interrupt)) try(lapply(X = S, FUN = FUN, ...), silent = TRUE) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 13: error <<- format(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
})14:
FUN(X[[i]], ...)
47: 15: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), lapply(seq_len(cores), inner.do) error = function(e) {
if (progress && is.function(pb$interrupt)) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 17: error <<- format(e)doTryCatch(return(expr), name, parentenv, handler)
18: }), list(rlang_trace_top_env = knit_global()))tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: 19: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt))
pb$interrupt()20: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, error <<- format(e) mc.preschedule = TRUE), error = function(e) NULL)
}), list(rlang_trace_top_env = knit_global())), function(loc) {21: setwd(wd)SweepApply(theta, worker, numProcess) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 22: paste0("\n", rule(), error, "\n", rule()))unlist(SweepApply(theta, worker, numProcess))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", process_file(text, output)
Traceback:
1:
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", RowCumsum(valid)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) E = E, showPlot = TRUE) 2:
51: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, eval(expr, envir)
52: tieBreak = FALSE, verbose = verbose)25: vweave_rmarkdown(...)eval(expr, envir)
53: 26: engine$weave(file, quiet = quiet, encoding = enc) 3:
withVisible(eval(expr, envir))54:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, doTryCatch(return(expr), name, parentenv, handler)27: tau = tau, theta = th, exclusionRadius = exclusionRadius, withCallingHandlers(code, error = function (e) embedded = embedded, validLib = validLib, noTime = noTime, rlang::entrace(e), message = function (cnd) ignoreNan = ignoreNan, backend = backend)
{55:
watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: if (on_message$capture) {ComputeError(predictions$Observations, predictions$Predictions)
watcher$push(cnd)56:
}tryCatchList(expr, classes, parentenv, handlers) if (on_message$silence) { 5:
invokeRestart("muffleMessage")SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 57: }tryCatch({ knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)}, warning = function (cnd) embedded = embedded, validLib = validLib, noTime = noTime, output <- find_vignette_product(name, by = "weave", engine = engine) ignoreNan = ignoreNan, backend = backend)$predictions){
if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) 6: output <- find_vignette_product(name, by = "texi2pdf", engine = engine) if (getOption("warn") >= 2 || getOption("warn") < 0) {FUN(X[[i]], ...) } return() outputs <- c(outputs, output) }}, error = function(e) { watcher$capture_plot_and_output() if (on_warning$capture) {
cnd <- sanitize_call(cnd) thisOK <<- FALSE watcher$push(cnd) } 7: if (on_warning$silence) {lapply(X = S, FUN = FUN, ...) fails <<- c(fails, file)
invokeRestart("muffleWarning") message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", } 8: }, error = function (cnd) file, conditionMessage(e)))doTryCatch(return(expr), name, parentenv, handler){}) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", stop = invokeRestart("eval_stop"), error = NULL)10: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpkxBBxx/filea15d20b9b58a.rds")tryCatchList(expr, classes, parentenv, handlers)})
An irrecoverable exception occurred. R is aborting now ...
11: 28: tryCatch(expr, error = function(e) {eval(call) call <- conditionCall(e) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 29: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)eval(call) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]30: with_handlers({ w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") for (expr in tle$exprs) { if (is.na(w)) ev <- withVisible(eval(expr, envir)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) type = "b") } if (w > LONG) TRUE prefix <- paste0(prefix, "\n ")}, handlers) }
else prefix <- "Error : "31: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())doWithOneRestart(return(expr), restart) }
invisible(structure(msg, class = "try-error", condition = e))32: })withOneRestart(expr, restarts[[1L]])
33: 12: withRestartList(expr, restarts[-nr])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
34: doWithOneRestart(return(expr), restart)13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
35: 14: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])FUN(X[[i]], ...)
15: 36: lapply(seq_len(cores), inner.do)withRestartList(expr, restarts)
16: 37: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()17: watcher$print_value(ev$value, ev$visible, envir)doTryCatch(return(expr), name, parentenv, handler) }
18: TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]])}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: 19: evaluate::evaluate(...)tryCatchList(expr, classes, parentenv, handlers)
39: 20: 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, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, stop_on_error = if (is.numeric(options$error)) options$error else { mc.preschedule = TRUE), error = function(e) NULL) if (options$error && options$include)
0L21: else 2LSweepApply(theta, worker, numProcess) }, output_handler = knit_handlers(options$render, options))
22: 40: unlist(SweepApply(theta, worker, numProcess))in_dir(input_dir(), expr)
23: 41: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", in_input_dir(evaluate(code, envir = env, new_device = FALSE, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 24: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0Leval(expr, envir) else 2L
}, output_handler = knit_handlers(options$render, options)))25:
eval(expr, envir)42:
26: eng_r(options)withVisible(eval(expr, envir))
27: 43: block_exec(params)withCallingHandlers(code, error = function (e)
44: rlang::entrace(e), message = function (cnd) call_block(x){ watcher$capture_plot_and_output() if (on_message$capture) {
watcher$push(cnd)45: }process_group(group) if (on_message$silence) {
invokeRestart("muffleMessage")46: }}, warning = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (progress && is.function(pb$interrupt)) return() } pb$interrupt() watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (on_warning$capture) { }) cnd <- sanitize_call(cnd)
watcher$push(cnd)47: }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (on_warning$silence) { error = function(e) { invokeRestart("muffleWarning") if (progress && is.function(pb$interrupt)) } pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)}, error = function (cnd) }), list(rlang_trace_top_env = knit_global())){
48: watcher$capture_plot_and_output()xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), cnd <- sanitize_call(cnd) error = function(e) { if (progress && is.function(pb$interrupt)) watcher$push(cnd) pb$interrupt() switch(on_error, continue = invokeRestart("eval_continue"), if (is_R_CMD_build() || is_R_CMD_check()) stop = invokeRestart("eval_stop"), error = NULL) 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)) 28: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)eval(call)
49: 29: process_file(text, output)eval(call)
50: 30: with_handlers({knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), watcher$capture_plot_and_output() output_dir = getwd(), ...) watcher$print_value(ev$value, ev$visible, envir)
}52: TRUEvweave_rmarkdown(...)}, handlers)
53: 31: engine$weave(file, quiet = quiet, encoding = enc)doWithOneRestart(return(expr), restart)
Traceback:
54: 1: doTryCatch(return(expr), name, parentenv, handler)RowCumsum(valid)32:
withOneRestart(expr, restarts[[1L]])
2: 33: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, withRestartList(expr, restarts[-nr]) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
55: 34: 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 35: ignoreNan = ignoreNan, backend = backend)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])56:
36: 4: tryCatchList(expr, classes, parentenv, handlers)ComputeError(predictions$Observations, predictions$Predictions)withRestartList(expr, restarts)
57:
tryCatch({37: 5: engine$weave(file, quiet = quiet, encoding = enc)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, setwd(startdir)withRestarts(with_handlers({ knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, for (expr in tle$exprs) { embedded = embedded, validLib = validLib, noTime = noTime, ev <- withVisible(eval(expr, envir)) ignoreNan = ignoreNan, backend = backend)$predictions) watcher$capture_plot_and_output() output <- find_vignette_product(name, by = "weave", engine = engine)
watcher$print_value(ev$value, ev$visible, envir) if (!have.makefile && vignette_is_tex(output)) { 6: texi2pdf(file = output, clean = FALSE, quiet = quiet)FUN(X[[i]], ...) } output <- find_vignette_product(name, by = "texi2pdf",
engine = engine) TRUE 7: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
lapply(X = S, FUN = FUN, ...)38:
outputs <- c(outputs, output)evaluate::evaluate(...) 8: }, error = function(e) {
thisOK <<- FALSEdoTryCatch(return(expr), name, parentenv, handler) fails <<- c(fails, file)
39: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 9: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, file, conditionMessage(e)))tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_message = if (is.numeric(options$message)) TRUE else options$message, })
stop_on_error = if (is.numeric(options$error)) options$error else {10:
if (options$error && options$include) tryCatchList(expr, classes, parentenv, handlers)58: 0Ltools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpkxBBxx/filea15d20b9b58a.rds") else 2L
}, output_handler = knit_handlers(options$render, options))
11: An irrecoverable exception occurred. R is aborting now ...
40: tryCatch(expr, error = function(e) {in_dir(input_dir(), expr) call <- conditionCall(e)
if (!is.null(call)) {41: if (identical(call[[1L]], quote(doTryCatch))) in_input_dir(evaluate(code, envir = env, new_device = FALSE, call <- sys.call(-4L) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, dcall <- deparse(call, nlines = 1L) stop_on_error = if (is.numeric(options$error)) options$error else { prefix <- paste("Error in", dcall, ": ") if (options$error && options$include) LONG <- 75L 0L sm <- strsplit(conditionMessage(e), "\n")[[1L]] else 2L w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") }, output_handler = knit_handlers(options$render, options))) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")42: if (w > LONG) eng_r(options) prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : "43: block_exec(params) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))44: if (!silent && isTRUE(getOption("show.error.messages"))) {call_block(x) cat(msg, file = outFile) .Internal(printDeferredWarnings())
}45: invisible(structure(msg, class = "try-error", condition = e))process_group(group)
})46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 12: error = function(e) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (progress && is.function(pb$interrupt))
pb$interrupt()13: if (is_R_CMD_build() || is_R_CMD_check()) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) error <<- format(e)
})14: FUN(X[[i]], ...)
47: 15: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {lapply(seq_len(cores), inner.do)
if (progress && is.function(pb$interrupt)) 16: pb$interrupt()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)17: doTryCatch(return(expr), name, parentenv, handler) }), list(rlang_trace_top_env = knit_global()))
18:
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 19: error = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt))
pb$interrupt()20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (is_R_CMD_build() || is_R_CMD_check()) mc.preschedule = TRUE), error = function(e) NULL) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {21: setwd(wd)SweepApply(theta, worker, numProcess) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 22: paste0("\n", rule(), error, "\n", rule()))unlist(SweepApply(theta, worker, numProcess))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: 23: process_file(text, output)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 50: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) E = E, showPlot = TRUE)
51: 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), eval(expr, envir) output_dir = getwd(), ...)
25: 52: eval(expr, envir)vweave_rmarkdown(...)
26:
withVisible(eval(expr, envir))53:
27: engine$weave(file, quiet = quiet, encoding = enc)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 54: {doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
if (on_message$capture) {55: watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
if (on_message$silence) {56: invokeRestart("muffleMessage")tryCatchList(expr, classes, parentenv, handlers) }
}, warning = function (cnd) 57: {tryCatch({ if (getOption("warn") >= 2 || getOption("warn") < 0) { engine$weave(file, quiet = quiet, encoding = enc) return() setwd(startdir) } output <- find_vignette_product(name, by = "weave", engine = engine) watcher$capture_plot_and_output() if (!have.makefile && vignette_is_tex(output)) { if (on_warning$capture) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", cnd <- sanitize_call(cnd) engine = engine) watcher$push(cnd) } } outputs <- c(outputs, output) if (on_warning$silence) {}, error = function(e) { invokeRestart("muffleWarning") thisOK <<- FALSE } fails <<- c(fails, file)}, error = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", { file, conditionMessage(e))) watcher$capture_plot_and_output()}) cnd <- sanitize_call(cnd)
watcher$push(cnd)58: switch(on_error, continue = invokeRestart("eval_continue"), tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpkxBBxx/filea15d20b9b58a.rds") stop = invokeRestart("eval_stop"), error = NULL)
An irrecoverable exception occurred. R is aborting now ...
})
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(), 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/RtmpkxBBxx/filea15d20b9b58a.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