Last updated on 2026-09-23 09:52:13 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.27 | 226.93 | 230.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.84 | 211.85 | 214.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.64 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.47 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 141.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.02 | 209.65 | 213.67 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.82 | 212.42 | 215.24 | 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 | 131.00 | 137.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 34.00 | 35.00 | 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 | 161.00 | 167.00 | 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
2026-09-23 15:31:40.195 R[50875:78540] 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$Predictions)
Traceback:
5: 1: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, RowCumsum(valid) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 2: ignoreNan = ignoreNan, backend = backend)$predictions)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 6: tieBreak = FALSE, verbose = verbose)FUN(X[[i]], ...)
3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 7: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, lapply(X = S, FUN = FUN, ...) ignoreNan = ignoreNan, backend = backend)
8: 4: doTryCatch(return(expr), name, parentenv, handler)ComputeError(predictions$Observations, predictions$Predictions)
9: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 10: embedded = embedded, validLib = validLib, noTime = noTime, tryCatchList(expr, classes, parentenv, handlers) ignoreNan = ignoreNan, backend = backend)$predictions)
Traceback:
1: 6: 11: RowCumsum(valid)tryCatch(expr, error = function(e) {FUN(X[[i]], ...) call <- conditionCall(e)
if (!is.null(call)) {
7: 2: if (identical(call[[1L]], quote(doTryCatch))) lapply(X = S, FUN = FUN, ...) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
prefix <- paste("Error in", dcall, ": ") validLib = validLib, libOverlap = idx$libOverlap, backend = backend, LONG <- 75L tieBreak = FALSE, verbose = verbose) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 8:
doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
9: 3: if (is.na(w)) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchOne(expr, names, parentenv, handlers[[1L]]) type = "b")
if (w > LONG) tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste0(prefix, "\n ") embedded = embedded, validLib = validLib, noTime = noTime, 10: } ignoreNan = ignoreNan, backend = backend)tryCatchList(expr, classes, parentenv, handlers) else prefix <- "Error : "
11: msg <- paste0(prefix, conditionMessage(e), "\n") 4: .Internal(seterrmessage(msg[1L]))ComputeError(predictions$Observations, predictions$Predictions)tryCatch(expr, error = function(e) { if (!silent && isTRUE(getOption("show.error.messages"))) { call <- conditionCall(e)
cat(msg, file = outFile) 5: if (!is.null(call)) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (identical(call[[1L]], quote(doTryCatch))) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, .Internal(printDeferredWarnings()) embedded = embedded, validLib = validLib, noTime = noTime, call <- sys.call(-4L) } ignoreNan = ignoreNan, backend = backend)$predictions) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") invisible(structure(msg, class = "try-error", condition = e)) 6: LONG <- 75L}) sm <- strsplit(conditionMessage(e), "\n")[[1L]]FUN(X[[i]], ...)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 7: if (is.na(w)) lapply(X = S, FUN = FUN, ...)12: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 8: type = "b")
doTryCatch(return(expr), name, parentenv, handler) if (w > LONG) 13: prefix <- paste0(prefix, "\n ")
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 9: }
tryCatchOne(expr, names, parentenv, handlers[[1L]])14: else prefix <- "Error : "
FUN(X[[i]], ...)10: msg <- paste0(prefix, conditionMessage(e), "\n")
tryCatchList(expr, classes, parentenv, handlers) .Internal(seterrmessage(msg[1L]))15: lapply(seq_len(cores), inner.do) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)11: 16: .Internal(printDeferredWarnings())parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatch(expr, error = function(e) { } call <- conditionCall(e)
if (!is.null(call)) {17: invisible(structure(msg, class = "try-error", condition = e)) if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler)}) call <- sys.call(-4L)
18: dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]])12:
prefix <- paste("Error in", dcall, ": ") LONG <- 75Ltry(lapply(X = S, FUN = FUN, ...), silent = TRUE) sm <- strsplit(conditionMessage(e), "\n")[[1L]]19:
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (is.na(w)) 20:
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 14: mc.preschedule = TRUE), error = function(e) NULL) type = "b")FUN(X[[i]], ...)
if (w > LONG)
21: 15: SweepApply(theta, worker, numProcess)
prefix <- paste0(prefix, "\n ")22: lapply(seq_len(cores), inner.do) }
unlist(SweepApply(theta, worker, numProcess))16: else prefix <- "Error : "parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
23: if (!silent && isTRUE(getOption("show.error.messages"))) {17: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", doTryCatch(return(expr), name, parentenv, handler) cat(msg, file = outFile)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", .Internal(printDeferredWarnings())18: } E = E, showPlot = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
})24: 19: eval(expr, envir)
12: tryCatchList(expr, classes, parentenv, handlers)25:
eval(expr, envir)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
20: 26: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, withVisible(eval(expr, envir))
mc.preschedule = TRUE), error = function(e) NULL)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))21:
Traceback:
27: 14: SweepApply(theta, worker, numProcess)FUN(X[[i]], ...) 1: withCallingHandlers(code, error = function (e)
15: RowCumsum(valid)rlang::entrace(e), message = function (cnd) 22:
lapply(seq_len(cores), inner.do) 2:
unlist(SweepApply(theta, worker, numProcess))16: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 23: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE){PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output()
if (on_message$capture) { tieBreak = FALSE, verbose = verbose) watcher$push(cnd)17: }doTryCatch(return(expr), name, parentenv, handler)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (on_message$silence) { E = E, showPlot = TRUE) invokeRestart("muffleMessage")18: tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
}, warning = function (cnd) embedded = embedded, validLib = validLib, noTime = noTime,
{ ignoreNan = ignoreNan, backend = backend)24: if (getOption("warn") >= 2 || getOption("warn") < 0) {19:
eval(expr, envir) 4: return()
}ComputeError(predictions$Observations, predictions$Predictions)25:
watcher$capture_plot_and_output()eval(expr, envir) 5: tryCatchList(expr, classes, parentenv, handlers) if (on_warning$capture) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, cnd <- sanitize_call(cnd)
watcher$push(cnd)
26: }20: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, embedded = embedded, validLib = validLib, noTime = noTime, withVisible(eval(expr, envir)) mc.preschedule = TRUE), error = function(e) NULL)
if (on_warning$silence) { ignoreNan = ignoreNan, backend = backend)$predictions) invokeRestart("muffleWarning")27:
}withCallingHandlers(code, error = function (e)
}, error = function (cnd) 6: {rlang::entrace(e), message = function (cnd) FUN(X[[i]], ...){21: watcher$capture_plot_and_output() watcher$capture_plot_and_output()
SweepApply(theta, worker, numProcess) 7: if (on_message$capture) {lapply(X = S, FUN = FUN, ...) watcher$push(cnd)
}22: if (on_message$silence) {unlist(SweepApply(theta, worker, numProcess)) invokeRestart("muffleMessage")
cnd <- sanitize_call(cnd) 8: }23: }, warning = function (cnd) watcher$push(cnd){PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", doTryCatch(return(expr), name, parentenv, handler) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (getOption("warn") >= 2 || getOption("warn") < 0) { E = E, showPlot = TRUE)
return() 9:
switch(on_error, continue = invokeRestart("eval_continue"), tryCatchOne(expr, names, parentenv, handlers[[1L]])24: stop = invokeRestart("eval_stop"), error = NULL)
eval(expr, envir)})10:
}25: 28: tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output()eval(expr, envir) if (on_warning$capture) {
eval(call)11: 26:
cnd <- sanitize_call(cnd)tryCatch(expr, error = function(e) {29: watcher$push(cnd) call <- conditionCall(e)withVisible(eval(expr, envir)) } if (!is.null(call)) {eval(call) if (on_warning$silence) { if (identical(call[[1L]], quote(doTryCatch)))
invokeRestart("muffleWarning") call <- sys.call(-4L)30:
with_handlers({ dcall <- deparse(call, nlines = 1L) } for (expr in tle$exprs) { prefix <- paste("Error in", dcall, ": ")}, error = function (cnd) 27: ev <- withVisible(eval(expr, envir)){withCallingHandlers(code, error = function (e) LONG <- 75L watcher$capture_plot_and_output() sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$print_value(ev$value, ev$visible, envir) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } TRUErlang::entrace(e), message = function (cnd) watcher$capture_plot_and_output(){ cnd <- sanitize_call(cnd) watcher$capture_plot_and_output() watcher$push(cnd) if (is.na(w)) if (on_message$capture) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$push(cnd)}, handlers) switch(on_error, continue = invokeRestart("eval_continue"), } type = "b") if (on_message$silence) {
invokeRestart("muffleMessage") if (w > LONG) } stop = invokeRestart("eval_stop"), error = NULL)}, warning = function (cnd) 31: {})doWithOneRestart(return(expr), restart) prefix <- paste0(prefix, "\n ")
if (getOption("warn") >= 2 || getOption("warn") < 0) {
32: }withOneRestart(expr, restarts[[1L]]) else prefix <- "Error : "
28: return()33: eval(call) }withRestartList(expr, restarts[-nr]) watcher$capture_plot_and_output()
msg <- paste0(prefix, conditionMessage(e), "\n")34: if (on_warning$capture) {doWithOneRestart(return(expr), restart)29: .Internal(seterrmessage(msg[1L]))eval(call) cnd <- sanitize_call(cnd)
watcher$push(cnd)35: if (!silent && isTRUE(getOption("show.error.messages"))) { }
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_warning$silence) {30: cat(msg, file = outFile)
.Internal(printDeferredWarnings())with_handlers({ invokeRestart("muffleWarning") for (expr in tle$exprs) {36: ev <- withVisible(eval(expr, envir)) }withRestartList(expr, restarts) } invisible(structure(msg, class = "try-error", condition = e)) watcher$capture_plot_and_output()}, error = function (cnd) watcher$print_value(ev$value, ev$visible, envir)})
}12: {37: watcher$capture_plot_and_output() TRUE cnd <- sanitize_call(cnd)}, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
withRestarts(with_handlers({
watcher$push(cnd)31: for (expr in tle$exprs) {doWithOneRestart(return(expr), restart) ev <- withVisible(eval(expr, envir))13: switch(on_error, continue = invokeRestart("eval_continue"),
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$capture_plot_and_output()
stop = invokeRestart("eval_stop"), error = NULL) watcher$print_value(ev$value, ev$visible, envir)})32:
withOneRestart(expr, restarts[[1L]])14:
33: }FUN(X[[i]], ...)28: withRestartList(expr, restarts[-nr])eval(call) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
15: 29: eval(call)34:
lapply(seq_len(cores), inner.do)38: doWithOneRestart(return(expr), restart)
evaluate::evaluate(...)
30: 35:
with_handlers({
for (expr in tle$exprs) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])39: ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withRestartList(expr, restarts) watcher$print_value(ev$value, ev$visible, envir)
16: keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else {37: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) TRUE if (options$error && options$include)
0L17: withRestarts(with_handlers({}, handlers)doTryCatch(return(expr), name, parentenv, handler) else 2L
for (expr in tle$exprs) {
18: ev <- withVisible(eval(expr, envir))31: }, output_handler = knit_handlers(options$render, options))doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)
}19: 32: TRUEtryCatchList(expr, classes, parentenv, handlers)40: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)in_dir(input_dir(), expr)withOneRestart(expr, restarts[[1L]])
33:
41: 20: 38: withRestartList(expr, restarts[-nr])in_input_dir(evaluate(code, envir = env, new_device = FALSE, tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
evaluate::evaluate(...) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 34:
mc.preschedule = TRUE), error = function(e) NULL)39:
keep_message = if (is.numeric(options$message)) TRUE else options$message, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, doWithOneRestart(return(expr), restart)21: stop_on_error = if (is.numeric(options$error)) options$error else { keep_message = if (is.numeric(options$message)) TRUE else options$message, SweepApply(theta, worker, numProcess)
stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 35: if (options$error && options$include) 22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 0L 0L
unlist(SweepApply(theta, worker, numProcess))36:
else 2L else 2L23: }, output_handler = knit_handlers(options$render, options))withRestartList(expr, restarts)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", }, output_handler = knit_handlers(options$render, options)))
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 37:
40: E = E, showPlot = TRUE)42: withRestarts(with_handlers({eng_r(options)in_dir(input_dir(), expr)
24: for (expr in tle$exprs) {41: eval(expr, envir)43: in_input_dir(evaluate(code, envir = env, new_device = FALSE, ev <- withVisible(eval(expr, envir))
block_exec(params) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$capture_plot_and_output()25: keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$print_value(ev$value, ev$visible, envir)
eval(expr, envir) stop_on_error = if (is.numeric(options$error)) options$error else { } if (options$error && options$include) TRUE
44: 0L}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)call_block(x) else 2L26:
}, output_handler = knit_handlers(options$render, options)))
38:
45: evaluate::evaluate(...)withVisible(eval(expr, envir))42:
process_group(group)eng_r(options)27:
withCallingHandlers(code, error = function (e) 39: 43: 46: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), rlang::entrace(e), message = function (cnd) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
{ error = function(e) {44: if (progress && is.function(pb$interrupt)) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output()call_block(x) pb$interrupt() if (on_message$capture) { stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) } if (options$error && options$include) error <<- format(e) if (on_message$silence) { 0L
}) else 2L invokeRestart("muffleMessage")45: } }, output_handler = knit_handlers(options$render, options))
process_group(group)40: 47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, warning = function (cnd) in_dir(input_dir(), expr)46:
error = function(e) {{withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 41: if (getOption("warn") >= 2 || getOption("warn") < 0) { error = function(e) { return() if (progress && is.function(pb$interrupt)) in_input_dir(evaluate(code, envir = env, new_device = FALSE, } if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, pb$interrupt() keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is_R_CMD_build() || is_R_CMD_check()) stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (options$error && options$include) error <<- format(e) 0L if (on_warning$capture) { else 2L }) cnd <- sanitize_call(cnd) }), list(rlang_trace_top_env = knit_global()))
watcher$push(cnd) }, output_handler = knit_handlers(options$render, options)))
47:
}42: if (on_warning$silence) {eng_r(options)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 48: error = function(e) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), invokeRestart("muffleWarning") error = function(e) { } if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) }, error = function (cnd) pb$interrupt()43: if (is_R_CMD_build() || is_R_CMD_check()) block_exec(params) pb$interrupt()
error <<- format(e)44: call_block(x) if (is_R_CMD_build() || is_R_CMD_check()) { }), list(rlang_trace_top_env = knit_global())) error <<- format(e)
watcher$capture_plot_and_output()
45: cnd <- sanitize_call(cnd) }), list(rlang_trace_top_env = knit_global())), function(loc) {process_group(group) setwd(wd)48: watcher$push(cnd)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), write_utf8(res, output %n% stdout()) error = function(e) { switch(on_error, continue = invokeRestart("eval_continue"), paste0("\nQuitting from ", loc, if (!is.null(error))
if (progress && is.function(pb$interrupt)) stop = invokeRestart("eval_stop"), error = NULL) paste0("\n", rule(), error, "\n", rule()))46: })}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt()
28: error = function(e) {49: if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) process_file(text, output) error <<- format(e)eval(call)
}), list(rlang_trace_top_env = knit_global())), function(loc) {
pb$interrupt()50: setwd(wd) if (is_R_CMD_build() || is_R_CMD_check()) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) write_utf8(res, output %n% stdout())29:
paste0("\nQuitting from ", loc, if (!is.null(error)) eval(call) error <<- format(e)51: paste0("\n", rule(), error, "\n", rule())) })
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 30: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
output_dir = getwd(), ...)
with_handlers({
47: for (expr in tle$exprs) {52: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 49: ev <- withVisible(eval(expr, envir)) error = function(e) { watcher$capture_plot_and_output()process_file(text, output)vweave_rmarkdown(...)
if (progress && is.function(pb$interrupt))
50: pb$interrupt()53: if (is_R_CMD_build() || is_R_CMD_check()) engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
error <<- format(e)51: 54: TRUErmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }), list(rlang_trace_top_env = knit_global()))}, handlers) output_dir = getwd(), ...)doTryCatch(return(expr), name, parentenv, handler)
31:
48: doWithOneRestart(return(expr), restart)52:
vweave_rmarkdown(...)
55: 53: tryCatchOne(expr, names, parentenv, handlers[[1L]])xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine$weave(file, quiet = quiet, encoding = enc)
32: 56: error = function(e) {
withOneRestart(expr, restarts[[1L]])54: if (progress && is.function(pb$interrupt)) doTryCatch(return(expr), name, parentenv, handler) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) tryCatchList(expr, classes, parentenv, handlers)33: error <<- format(e)55:
}), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestartList(expr, restarts[-nr]) setwd(wd)
write_utf8(res, output %n% stdout())56: paste0("\nQuitting from ", loc, if (!is.null(error))
57: paste0("\n", rule(), error, "\n", rule()))34: tryCatchList(expr, classes, parentenv, handlers)tryCatch({doWithOneRestart(return(expr), restart)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
engine$weave(file, quiet = quiet, encoding = enc)
57: 35: setwd(startdir)tryCatch({withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])49: engine$weave(file, quiet = quiet, encoding = enc) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {36: setwd(startdir) texi2pdf(file = output, clean = FALSE, quiet = quiet)withRestartList(expr, restarts) output <- find_vignette_product(name, by = "texi2pdf", output <- find_vignette_product(name, by = "weave", engine = engine)process_file(text, output) engine = engine) if (!have.makefile && vignette_is_tex(output)) {
37: } texi2pdf(file = output, clean = FALSE, quiet = quiet)withRestarts(with_handlers({50: output <- find_vignette_product(name, by = "texi2pdf", outputs <- c(outputs, output) for (expr in tle$exprs) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)}, error = function(e) { ev <- withVisible(eval(expr, envir)) engine = engine)
} watcher$capture_plot_and_output() outputs <- c(outputs, output)51: }, error = function(e) { watcher$print_value(ev$value, ev$visible, envir) thisOK <<- FALSErmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } thisOK <<- FALSE fails <<- c(fails, file) output_dir = getwd(), ...) TRUE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) file, conditionMessage(e))) file, conditionMessage(e)))
})})52:
vweave_rmarkdown(...)
38: 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/RtmpTsNifE/filea510683ff016.rds")58:
evaluate::evaluate(...)
53: An irrecoverable exception occurred. R is aborting now ...
39: engine$weave(file, quiet = quiet, encoding = enc)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
keep_message = if (is.numeric(options$message)) TRUE else options$message, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpTsNifE/filea510683ff016.rds")54: stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler) 0L
An irrecoverable exception occurred. R is aborting now ...
55: else 2LtryCatchOne(expr, names, parentenv, handlers[[1L]]) }, output_handler = knit_handlers(options$render, options))
40: 56: in_dir(input_dir(), expr)tryCatchList(expr, classes, parentenv, handlers)
41: 57: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch({ keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) stop_on_error = if (is.numeric(options$error)) options$error else { output <- find_vignette_product(name, by = "weave", engine = engine) if (options$error && options$include) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) 0L } else 2L outputs <- c(outputs, output) }, output_handler = knit_handlers(options$render, options)))}, error = function(e) {
thisOK <<- FALSE42: fails <<- c(fails, file)eng_r(options) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))43: })block_exec(params)
58: 44: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpTsNifE/filea510683ff016.rds")call_block(x)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpTsNifE/filea510683ff016.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