Last updated on 2026-10-11 04:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.49 | 219.56 | 223.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.54 | 231.12 | 233.66 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.60 | 213.69 | 217.29 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.18 | 212.69 | 215.87 | 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 | 5.00 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 35.00 | 37.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 163.00 | 170.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-10-11 14:08:47.647 R[47253:70066] XType: Using static font registry.
*** 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$libOverlap, backend = backend,
*** caught segfault ***
address 0x110, cause 'invalid permissions'
tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26:
*** caught segfault ***
withVisible(eval(expr, envir))address 0x110, cause 'invalid permissions'
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 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/RtmpQdmnEO/file8481640ace92.rds")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30:
Traceback:
1: with_handlers({RowCumsum(valid) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() 2: watcher$print_value(ev$value, ev$visible, envir) }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, TRUE tieBreak = FALSE, verbose = verbose)
}, handlers) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 31: doWithOneRestart(return(expr), restart) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)32:
4: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])ComputeError(predictions$Observations, predictions$Predictions)
34: doWithOneRestart(return(expr), restart)
5: 35: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 36: embedded = embedded, validLib = validLib, noTime = noTime, withRestartList(expr, restarts)
ignoreNan = ignoreNan, backend = backend)$predictions)37:
withRestarts(with_handlers({ 6: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))FUN(X[[i]], ...)
watcher$capture_plot_and_output() 7: watcher$print_value(ev$value, ev$visible, envir) } TRUElapply(X = S, FUN = FUN, ...)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 8:
38: doTryCatch(return(expr), name, parentenv, handler)evaluate::evaluate(...)
9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 10: tryCatchList(expr, classes, parentenv, handlers) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {11: if (options$error && options$include) tryCatch(expr, error = function(e) { 0L call <- conditionCall(e) else 2L if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) }, output_handler = knit_handlers(options$render, options)) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")40: in_dir(input_dir(), expr) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (is.na(w)) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { type = "b") if (w > LONG) if (options$error && options$include) prefix <- paste0(prefix, "\n ") 0L } else prefix <- "Error : " else 2L }, output_handler = knit_handlers(options$render, options))) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))42: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)eng_r(options) .Internal(printDeferredWarnings())
}43: invisible(structure(msg, class = "try-error", condition = e))block_exec(params)})
44: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)call_block(x)
13: 45: process_group(group)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
46: 14: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), FUN(X[[i]], ...) error = function(e) {
if (progress && is.function(pb$interrupt)) 15: lapply(seq_len(cores), inner.do) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
16: error <<- format(e)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
})
17: doTryCatch(return(expr), name, parentenv, handler)
47: 18: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt()19: if (is_R_CMD_build() || is_R_CMD_check()) tryCatchList(expr, classes, parentenv, handlers)
error <<- format(e)20: }), list(rlang_trace_top_env = knit_global()))
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 48: mc.preschedule = TRUE), error = function(e) NULL)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 21: error = function(e) {SweepApply(theta, worker, numProcess) if (progress && is.function(pb$interrupt))
pb$interrupt()22: unlist(SweepApply(theta, worker, numProcess)) if (is_R_CMD_build() || is_R_CMD_check())
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", error <<- format(e) E = E, showPlot = TRUE)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)24: write_utf8(res, output %n% stdout())eval(expr, envir) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))
25: eval(expr, envir)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)26:
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)withVisible(eval(expr, envir))
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: 27: vweave_rmarkdown(...)withCallingHandlers(code, error = function (e)
53: rlang::entrace(e), message = function (cnd) engine$weave(file, quiet = quiet, encoding = enc){
watcher$capture_plot_and_output()54: if (on_message$capture) {doTryCatch(return(expr), name, parentenv, handler) watcher$push(cnd)
55: }tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (on_message$silence) {56: invokeRestart("muffleMessage")tryCatchList(expr, classes, parentenv, handlers) }
}, warning = function (cnd) 57: {tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) if (getOption("warn") >= 2 || getOption("warn") < 0) { setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { return() texi2pdf(file = output, clean = FALSE, quiet = quiet) } output <- find_vignette_product(name, by = "texi2pdf", engine = engine) watcher$capture_plot_and_output() } outputs <- c(outputs, output) if (on_warning$capture) {}, error = function(e) { thisOK <<- FALSE cnd <- sanitize_call(cnd) fails <<- c(fails, file) watcher$push(cnd) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (on_warning$silence) { file, conditionMessage(e)))}) invokeRestart("muffleWarning")
}58: }, error = function (cnd) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpQdmnEO/file8481640ace92.rds")
watcher$capture_plot_and_output()An irrecoverable exception occurred. R is aborting now ...
cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L
Traceback:
1: else 2LRowCumsum(valid) }, output_handler = knit_handlers(options$render, options))
2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 40: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, in_dir(input_dir(), expr) tieBreak = FALSE, verbose = verbose)
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 3: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, keep_message = if (is.numeric(options$message)) TRUE else options$message, tau = tau, theta = th, exclusionRadius = exclusionRadius, stop_on_error = if (is.numeric(options$error)) options$error else { embedded = embedded, validLib = validLib, noTime = noTime, if (options$error && options$include) ignoreNan = ignoreNan, backend = backend)
0L else 2L }, output_handler = knit_handlers(options$render, options)))
4: 42: ComputeError(predictions$Observations, predictions$Predictions)eng_r(options)
5: 43: block_exec(params)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
44: embedded = embedded, validLib = validLib, noTime = noTime, call_block(x) ignoreNan = ignoreNan, backend = backend)$predictions)
45: 6: process_group(group)FUN(X[[i]], ...)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 7: if (progress && is.function(pb$interrupt)) lapply(X = S, FUN = FUN, ...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 8: error <<- format(e)doTryCatch(return(expr), name, parentenv, handler)
}) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 10: tryCatchList(expr, classes, parentenv, handlers) error = function(e) {
if (progress && is.function(pb$interrupt)) 11: pb$interrupt()tryCatch(expr, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) call <- conditionCall(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 48: call <- sys.call(-4L)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), dcall <- deparse(call, nlines = 1L) error = function(e) { prefix <- paste("Error in", dcall, ": ") LONG <- 75L if (progress && is.function(pb$interrupt)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] pb$interrupt() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (is.na(w)) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], paste0("\nQuitting from ", loc, if (!is.null(error)) type = "b") paste0("\n", rule(), error, "\n", rule())) if (w > LONG) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) prefix <- paste0(prefix, "\n ")
49: process_file(text, output) }
else prefix <- "Error : "50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))51: if (!silent && isTRUE(getOption("show.error.messages"))) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
cat(msg, file = outFile)52: .Internal(printDeferredWarnings()) }vweave_rmarkdown(...) invisible(structure(msg, class = "try-error", condition = e))
})
53: 12: engine$weave(file, quiet = quiet, encoding = enc)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))54:
doTryCatch(return(expr), name, parentenv, handler)14:
FUN(X[[i]], ...)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])15:
lapply(seq_len(cores), inner.do)56:
tryCatchList(expr, classes, parentenv, handlers)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)57:
17: doTryCatch(return(expr), name, parentenv, handler)tryCatch({
18: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {19: tryCatchList(expr, classes, parentenv, handlers) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 20: engine = engine)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) }
outputs <- c(outputs, output)21: }, error = function(e) {SweepApply(theta, worker, numProcess)
thisOK <<- FALSE22: fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", unlist(SweepApply(theta, worker, numProcess))
file, conditionMessage(e)))23: })PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: 58: eval(expr, envir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
25: eval(expr, envir)
26: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpQdmnEO/file8481640ace92.rds")withVisible(eval(expr, envir))
27: An irrecoverable exception occurred. R is aborting now ...
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 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/RtmpQdmnEO/file8481640ace92.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