Last updated on 2026-08-18 04:50:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.57 | 226.18 | 229.75 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.70 | 225.97 | 228.67 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 4.00 | 257.00 | 261.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.27 | 210.37 | 213.64 | 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 | 0.00 | 6.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 40.00 | 41.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 8.00 | 165.00 | 173.00 | 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
2026-08-18 10:23:32.207 R[41061:59745] 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$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$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:
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$Predictions)
5: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
Traceback:
1: RowCumsum(valid)tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
Traceback:
21: SweepApply(theta, worker, numProcess) 1:
RowCumsum(valid)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) 2:
6: 25: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, eval(expr, envir) 2:
verbose = verbose)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 26: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: 8: doTryCatch(return(expr), name, parentenv, handler)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
3: 9: tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: embedded = embedded, validLib = validLib, noTime = noTime, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 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], tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend) type = "b") if (w > LONG) withVisible(eval(expr, envir))
embedded = embedded, validLib = validLib, noTime = noTime, 27:
prefix <- paste0(prefix, "\n ") ignoreNan = ignoreNan, backend = backend)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { }
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)$predictions)
watcher$push(cnd) 4: } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) ComputeError(predictions$Observations, predictions$Predictions){ if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
else prefix <- "Error : " 6: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { } 5: watcher$capture_plot_and_output() cat(msg, file = outFile)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)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: .Internal(printDeferredWarnings())doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...) if (on_warning$capture) { }
7: 9: cnd <- sanitize_call(cnd) watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
15:
lapply(seq_len(cores), inner.do)
if (on_warning$silence) {16: invokeRestart("muffleWarning") }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)10:
}, error = function (cnd) { watcher$capture_plot_and_output()17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: 8: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {19: cnd <- sanitize_call(cnd) watcher$push(cnd)
call <- conditionCall(e) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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) switch(on_error, continue = invokeRestart("eval_continue"), 10: stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)tryCatchList(expr, classes, parentenv, handlers) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")29: .Internal(seterrmessage(msg[1L]))20: 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$visible, envir) } TRUE}, handlers)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 31: if (!silent && isTRUE(getOption("show.error.messages"))) {doWithOneRestart(return(expr), restart) mc.preschedule = TRUE), error = function(e) NULL)
cat(msg, file = outFile)tryCatchList(expr, classes, parentenv, handlers) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {32: }) if (identical(call[[1L]], quote(doTryCatch)))
withOneRestart(expr, restarts[[1L]])
21: 33: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)withRestartList(expr, restarts[-nr])SweepApply(theta, worker, numProcess)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13:
34: doWithOneRestart(return(expr), restart)22:
prefix <- paste("Error in", dcall, ": ")unlist(SweepApply(theta, worker, numProcess))35: LONG <- 75LsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG)
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
prefix <- paste0(prefix, "\n ")14: 24: }FUN(X[[i]], ...)36:
15: withRestartList(expr, restarts)eval(expr, envir) else prefix <- "Error : "
37: lapply(seq_len(cores), inner.do)25: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {eval(expr, envir) cat(msg, file = outFile)
withRestarts(with_handlers({26:
16: .Internal(printDeferredWarnings()) for (expr in tle$exprs) {withVisible(eval(expr, envir)) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)27: }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)withCallingHandlers(code, error = function (e)
invisible(structure(msg, class = "try-error", condition = e))rlang::entrace(e), message = function (cnd) }){20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$capture_plot_and_output() mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", } TRUE
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) E = E, showPlot = TRUE)
if (on_message$capture) {
24: 13: watcher$push(cnd) }eval(expr, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
if (on_message$silence) {25: 15: 38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(expr, envir) invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }
26: withVisible(eval(expr, envir)) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) if (on_warning$capture) {
cnd <- sanitize_call(cnd)40:
in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, lapply(seq_len(cores), inner.do)27: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withCallingHandlers(code, error = function (e) watcher$push(cnd)
rlang::entrace(e), message = function (cnd) { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() } if (on_message$capture) { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) if (on_warning$silence) { watcher$push(cnd)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]]) if (on_message$silence) { 0L invokeRestart("muffleWarning")
}}, error = function (cnd) else 2L }, output_handler = knit_handlers(options$render, options)))
invokeRestart("muffleMessage") }}, warning = function (cnd) 42: eng_r(options){{
43: block_exec(params)
if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$capture_plot_and_output()44: cnd <- sanitize_call(cnd) watcher$push(cnd) return()19: tryCatchList(expr, classes, parentenv, handlers)
20: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() if (on_warning$capture) { error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, cnd <- sanitize_call(cnd) stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd) })}) }
mc.preschedule = TRUE), error = function(e) NULL)
47:
21: if (on_warning$silence) {28: invokeRestart("muffleWarning")eval(call)
}}, error = function (cnd) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 29: SweepApply(theta, worker, numProcess){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$visible, envir) } watcher$capture_plot_and_output() TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
cnd <- sanitize_call(cnd)
error = function(e) { watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), 22: unlist(SweepApply(theta, worker, numProcess))
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]) if (progress && is.function(pb$interrupt))
pb$interrupt() stop = invokeRestart("eval_stop"), error = NULL)34: })
doWithOneRestart(return(expr), restart)28: 23:
35: if (is_R_CMD_build() || is_R_CMD_check()) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))eval(call) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
36: withRestartList(expr, restarts)
37: 29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) E = E, showPlot = TRUE)withRestarts(with_handlers({
watcher$capture_plot_and_output()24: watcher$print_value(ev$value, ev$visible, envir) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) }48: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }eval(expr, envir) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, error = function(e) {25: eval(expr, envir)
TRUE26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { if (progress && is.function(pb$interrupt)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) pb$interrupt() 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
watcher$capture_plot_and_output()}, handlers) if (on_message$capture) { watcher$push(cnd)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, } if (on_message$silence) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()31: doWithOneRestart(return(expr), restart)
32: keep_message = if (is.numeric(options$message)) TRUE else options$message, withOneRestart(expr, restarts[[1L]]) if (is_R_CMD_build() || is_R_CMD_check()) } watcher$capture_plot_and_output()
error <<- format(e)33: if (on_warning$capture) { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) withRestartList(expr, restarts[-nr]) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }), list(rlang_trace_top_env = knit_global())), function(loc) { 0L else 2L setwd(wd) }, output_handler = knit_handlers(options$render, options))) write_utf8(res, output %n% stdout()) }}, error = function (cnd)
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))
paste0("\nQuitting from ", loc, if (!is.null(error)) pb$interrupt() paste0("\n", rule(), error, "\n", rule())) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc){
49: process_file(text, output) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) })
watcher$push(cnd)34: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
28: 49: eval(call)
29: eval(call)process_file(text, output)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36:
50: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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$render, options))
40: in_dir(input_dir(), expr)
41:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52:
vweave_rmarkdown(...)30: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
53: with_handlers({engine$weave(file, quiet = quiet, encoding = enc) for (expr in tle$exprs) {
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: 54: 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)doTryCatch(return(expr), name, parentenv, handler) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
55: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_message = if (is.numeric(options$message)) TRUE else options$message,
55: 56: 32: stop_on_error = if (is.numeric(options$error)) options$error else {withOneRestart(expr, restarts[[1L]]) if (options$error && options$include) tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!have.makefile && vignette_is_tex(output)) {33: texi2pdf(file = output, clean = FALSE, quiet = quiet)
0LwithRestartList(expr, restarts[-nr]) output <- find_vignette_product(name, by = "texi2pdf", 56: engine = engine) }tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) outputs <- c(outputs, output)}, error = function(e) {
else 2L }, output_handler = knit_handlers(options$render, options)))}, error = function(e) { thisOK <<- FALSE
34: fails <<- c(fails, file)doWithOneRestart(return(expr), restart)
42: thisOK <<- FALSE35: fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})eng_r(options)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
43: block_exec(params)
44: call_block(x)
45: process_group(group)
58: 46:
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() file, conditionMessage(e))) error = function(e) { if (progress && is.function(pb$interrupt)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", })
58: watcher$print_value(ev$value, ev$visible, envir) } TRUE pb$interrupt()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpeqBs3R/file6a351edd338f.rds") 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) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpeqBs3R/file6a351edd338f.rds")
An irrecoverable exception occurred. R is aborting now ...
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$render, options))
An irrecoverable exception occurred. R is aborting now ...
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) pb$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(...) 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:
53: engine$weave(file, quiet = quiet, encoding = enc)
vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
54: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) engine$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) 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", 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))) 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/RtmpeqBs3R/file6a351edd338f.rds")})
58:
An irrecoverable exception occurred. R is aborting now ...
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpeqBs3R/file6a351edd338f.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