Last updated on 2026-08-09 04:49:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.35 | 222.44 | 225.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.42 | 231.46 | 233.88 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 186.14 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 131.00 | 136.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 3.74 | 206.25 | 209.99 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.45 | 205.25 | 208.70 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 43.00 | 44.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 5.00 | 164.00 | 169.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-09 10:55:17.171 R[40300:58757] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
Traceback:
1: RowCumsum(valid) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 5: tryCatch(expr, error = function(e) { call <- conditionCall(e)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
Traceback:
1: RowCumsum(valid) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") embedded = embedded, validLib = validLib, noTime = noTime,
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") ignoreNan = ignoreNan, backend = backend)$predictions) if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") verbose = verbose)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { 3: cat(msg, file = outFile)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
8: doTryCatch(return(expr), name, parentenv, handler)
9: .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") 4: })
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
15: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
ComputeError(predictions$Observations, predictions$Predictions)14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)lapply(seq_len(cores), inner.do)
8: 16: doTryCatch(return(expr), name, parentenv, handler)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: 10: doTryCatch(return(expr), name, parentenv, handler)
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)tryCatchList(expr, classes, parentenv, handlers)
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: 11: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (on_message$capture) { 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")18: watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (w > LONG) } prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (on_message$silence) { invokeRestart("muffleMessage")
Traceback:
19: tryCatchList(expr, classes, parentenv, handlers)
20: 1: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }RowCumsum(valid) cat(msg, file = outFile)}, warning = function (cnd) .Internal(printDeferredWarnings())
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, mc.preschedule = TRUE), error = function(e) NULL){ if (getOption("warn") >= 2 || getOption("warn") < 0) {
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }21: verbose = verbose)
3: return() invisible(structure(msg, class = "try-error", condition = e))SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, })SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
} watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) tau = tau, theta = th, exclusionRadius = exclusionRadius, }
if (on_warning$silence) {23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
12: embedded = embedded, validLib = validLib, noTime = noTime, 24: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) ignoreNan = ignoreNan, backend = backend)
4: invokeRestart("muffleWarning")eval(expr, envir)
25: ComputeError(predictions$Observations, predictions$Predictions)eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()
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)$predictions) if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { }
}, error = function (cnd) {13: watcher$capture_plot_and_output() 6: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
FUN(X[[i]], ...) invokeRestart("muffleMessage") }
cnd <- sanitize_call(cnd) 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
}, warning = function (cnd) 14: { watcher$push(cnd) 9: FUN(X[[i]], ...) if (getOption("warn") >= 2 || getOption("warn") < 0) {
15: switch(on_error, continue = invokeRestart("eval_continue"), return()lapply(seq_len(cores), inner.do) stop = invokeRestart("eval_stop"), error = NULL)})
28: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()eval(call)
16:
if (on_warning$capture) {29: 10: tryCatchList(expr, classes, parentenv, handlers)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)eval(call)11: cnd <- sanitize_call(cnd) watcher$push(cnd) }
if (on_warning$silence) {17: doTryCatch(return(expr), name, parentenv, handler)
30: 18: invokeRestart("muffleWarning")with_handlers({ }}, 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: tryCatch(expr, error = function(e) {eval(call)
29: eval(call) for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
call <- conditionCall(e)
if (!is.null(call)) {19: 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) if (identical(call[[1L]], quote(doTryCatch))) 31: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
watcher$capture_plot_and_output()21: watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)SweepApply(theta, worker, numProcess)doWithOneRestart(return(expr), restart)
LONG <- 75L22: 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)31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: sm <- strsplit(conditionMessage(e), "\n")[[1L]]
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])26: doWithOneRestart(return(expr), restart)withVisible(eval(expr, envir))
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$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {
watcher$capture_plot_and_output() if (on_message$capture) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") watcher$push(cnd) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (on_message$silence) {38: type = "b")34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) invokeRestart("muffleMessage")evaluate::evaluate(...) if (w > LONG)
39:
prefix <- paste0(prefix, "\n ") }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, warning = function (cnd) } keep_message = if (is.numeric(options$message)) TRUE else options$message, else prefix <- "Error : "{ msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (getOption("warn") >= 2 || getOption("warn") < 0) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) }) return()
} watcher$capture_plot_and_output() 0L36: else 2L if (on_warning$capture) {12: cnd <- sanitize_call(cnd) watcher$push(cnd) } }, output_handler = knit_handlers(options$render, options)) if (on_warning$silence) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
invokeRestart("muffleWarning")13: }}, 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)})
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))28: 40: eval(call)
29: eval(call)
30: with_handlers({in_dir(input_dir(), expr) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
14: FUN(X[[i]], ...)
15: withRestartList(expr, restarts)
37: lapply(seq_len(cores), inner.do)
withRestarts(with_handlers({16:
for (expr in tle$exprs) {37: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)41: withRestarts(with_handlers({in_input_dir(evaluate(code, envir = env, new_device = FALSE, for (expr in tle$exprs) {
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: ev <- withVisible(eval(expr, envir)) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)tryCatchList(expr, classes, parentenv, handlers) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
20:
38: } keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUEtryCatch(parallel::mclapply(values, worker, mc.cores = cores, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...)
38: mc.preschedule = TRUE), error = function(e) NULL)
if (options$error && options$include) 39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, evaluate::evaluate(...)21: SweepApply(theta, worker, numProcess) stop_on_error = if (is.numeric(options$error)) options$error else {
22: unlist(SweepApply(theta, worker, numProcess))
0L else 2L
if (options$error && options$include) 39: 0L else 2L }, output_handler = knit_handlers(options$render, options))23: }, output_handler = knit_handlers(options$render, options)))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24:
keep_message = if (is.numeric(options$message)) TRUE else options$message, 40: stop_on_error = if (is.numeric(options$error)) options$error else {eval(expr, envir) if (options$error && options$include)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
0L else 2L
in_dir(input_dir(), expr)27: }, output_handler = knit_handlers(options$render, options))
40: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) in_dir(input_dir(), expr){
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
42: eng_r(options)41: 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) in_input_dir(evaluate(code, envir = env, new_device = FALSE, 0L keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, else 2L
43: block_exec(params)
44: keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options))) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0Lcall_block(x)
45: process_group(group)
if (on_message$capture) { else 2L
46: }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call_block(x) watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }
45: process_group(group)42: error = function(e) {}, warning = function (cnd) {
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (getOption("warn") >= 2 || getOption("warn") < 0) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })eng_r(options)
if (progress && is.function(pb$interrupt)) 47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 43: block_exec(params)
pb$interrupt() error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)44: }) return()call_block(x)
if (progress && is.function(pb$interrupt)) 45: pb$interrupt()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)
} if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) watcher$capture_plot_and_output() })
47: if (on_warning$capture) {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())) cnd <- sanitize_call(cnd)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) }
if (on_warning$silence) { invokeRestart("muffleWarning") }), 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() }48: error = function(e) {}, error = function (cnd) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) error <<- format(e) error = function(e) { switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global()))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 48: })
28: error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout())eval(call) if (is_R_CMD_build() || is_R_CMD_check())
29: eval(call)
30: 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() paste0("\nQuitting from ", loc, if (!is.null(error)) error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) with_handlers({ }), list(rlang_trace_top_env = knit_global())), function(loc) { for (expr in tle$exprs) { error <<- format(e) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) }), list(rlang_trace_top_env = knit_global())), function(loc) { paste0("\n", rule(), error, "\n", rule())) setwd(wd) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$print_value(ev$value, ev$visible, envir) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)49: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
}49: TRUE}, handlers)
31: process_file(text, output)process_file(text, output)doWithOneRestart(return(expr), restart)
50: 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
32: 51: output_dir = getwd(), ...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 51:
output_dir = getwd(), ...)52: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), vweave_rmarkdown(...)
output_dir = getwd(), ...)withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36:
52: withRestartList(expr, restarts)
37: 53: engine$weave(file, quiet = quiet, encoding = enc)withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()vweave_rmarkdown(...) watcher$print_value(ev$value, ev$visible, envir)52: vweave_rmarkdown(...)
53: }
engine$weave(file, quiet = quiet, encoding = enc)
TRUE
53: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)engine$weave(file, quiet = quiet, encoding = enc)
54: 54: doTryCatch(return(expr), name, parentenv, handler)
54: doTryCatch(return(expr), name, parentenv, handler)
38: evaluate::evaluate(...)doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])39:
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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",
55: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 55: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdDeJrj/file6b312be3037d.rds")
tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_message = if (is.numeric(options$message)) TRUE else options$message, An irrecoverable exception occurred. R is aborting now ...
stop_on_error = if (is.numeric(options$error)) options$error else {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (options$error && options$include)
56: tryCatchList(expr, classes, parentenv, handlers)
0L57: else 2LtryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)56: tryCatchList(expr, classes, parentenv, handlers) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
57: tryCatch({ engine$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 }, output_handler = knit_handlers(options$render, options)) fails <<- c(fails, file)
40: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdDeJrj/file6b312be3037d.rds")
An irrecoverable exception occurred. R is aborting now ...
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdDeJrj/file6b312be3037d.rds")
An irrecoverable exception occurred. R is aborting now ...
in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/RtmpdDeJrj/file6b312be3037d.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