Last updated on 2026-10-17 10:51:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.66 | 225.50 | 229.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.47 | 224.20 | 226.67 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 137.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | 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 | 6.00 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 38.00 | 39.00 | 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 | 158.00 | 165.00 | 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
2026-10-17 20:57:35.258 R[44641:68245] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
*** caught segfault ***
tau = tau, theta = th, exclusionRadius = exclusionRadius, address 0x110, cause 'invalid permissions'
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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())
Traceback:
error <<- format(e) 1: }), list(rlang_trace_top_env = knit_global())), function(loc) {RowCumsum(valid) setwd(wd)
write_utf8(res, output %n% stdout()) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, paste0("\nQuitting from ", loc, if (!is.null(error)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) tieBreak = FALSE, verbose = verbose)
49: 3: process_file(text, output)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 50: embedded = embedded, validLib = validLib, noTime = noTime, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) ignoreNan = ignoreNan, backend = backend)
4: 51: ComputeError(predictions$Observations, predictions$Predictions)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 52: vweave_rmarkdown(...) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
53: embedded = embedded, validLib = validLib, noTime = noTime, engine$weave(file, quiet = quiet, encoding = enc) ignoreNan = ignoreNan, backend = backend)$predictions)
54: 6: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
7: 55: lapply(X = S, FUN = FUN, ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers) 8:
57: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatch({tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)10: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchList(expr, classes, parentenv, handlers)
if (!have.makefile && vignette_is_tex(output)) {11: texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatch(expr, error = function(e) { call <- conditionCall(e) output <- find_vignette_product(name, by = "texi2pdf", if (!is.null(call)) { engine = engine) if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) outputs <- c(outputs, output) dcall <- deparse(call, nlines = 1L)}, error = function(e) { prefix <- paste("Error in", dcall, ": ") thisOK <<- FALSE fails <<- c(fails, file) LONG <- 75L message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", sm <- strsplit(conditionMessage(e), "\n")[[1L]] file, conditionMessage(e))) 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")58: if (w > LONG) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", prefix <- paste0(prefix, "\n ") skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp9A80f9/file8c0076e16a3a.rds")
}An irrecoverable exception occurred. R is aborting now ...
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:
Traceback:
eval(expr, envir) 1:
RowCumsum(valid)25:
eval(expr, envir) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 26: withVisible(eval(expr, envir)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)27:
3: withCallingHandlers(code, error = function (e) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, rlang::entrace(e), message = function (cnd) tau = tau, theta = th, exclusionRadius = exclusionRadius, { embedded = embedded, validLib = validLib, noTime = noTime, watcher$capture_plot_and_output() ignoreNan = ignoreNan, backend = backend) if (on_message$capture) {
watcher$push(cnd) 4: } if (on_message$silence) {ComputeError(predictions$Observations, predictions$Predictions) invokeRestart("muffleMessage")
} 5: }, warning = function (cnd) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, { if (getOption("warn") >= 2 || getOption("warn") < 0) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, return() embedded = embedded, validLib = validLib, noTime = noTime, } ignoreNan = ignoreNan, backend = backend)$predictions) watcher$capture_plot_and_output()
if (on_warning$capture) { 6: cnd <- sanitize_call(cnd)FUN(X[[i]], ...) watcher$push(cnd)
7: }lapply(X = S, FUN = FUN, ...)
if (on_warning$silence) { invokeRestart("muffleWarning") } 8: }, error = function (cnd) doTryCatch(return(expr), name, parentenv, handler){
9: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) cnd <- sanitize_call(cnd)
watcher$push(cnd)10: switch(on_error, continue = invokeRestart("eval_continue"), tryCatchList(expr, classes, parentenv, handlers) stop = invokeRestart("eval_stop"), error = NULL)
11: })tryCatch(expr, error = function(e) {
call <- conditionCall(e)28: if (!is.null(call)) {eval(call)
if (identical(call[[1L]], quote(doTryCatch))) 29: call <- sys.call(-4L)eval(call) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")30: LONG <- 75Lwith_handlers({ sm <- strsplit(conditionMessage(e), "\n")[[1L]] for (expr in tle$exprs) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") ev <- withVisible(eval(expr, envir)) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$print_value(ev$value, ev$visible, envir) type = "b") } if (w > LONG) TRUE prefix <- paste0(prefix, "\n ")}, handlers) }
31: doWithOneRestart(return(expr), restart) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")32: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {withOneRestart(expr, restarts[[1L]]) cat(msg, file = outFile)
.Internal(printDeferredWarnings())33: }withRestartList(expr, restarts[-nr]) invisible(structure(msg, class = "try-error", condition = e))
})34:
doWithOneRestart(return(expr), restart)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
36: 14: withRestartList(expr, restarts)FUN(X[[i]], ...)
37: 15: withRestarts(with_handlers({lapply(seq_len(cores), inner.do) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))16: watcher$capture_plot_and_output()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$print_value(ev$value, ev$visible, envir)
}17: TRUEdoTryCatch(return(expr), name, parentenv, handler)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
*** caught segfault ***
38:
evaluate::evaluate(...)18: address 0x110, cause 'invalid permissions'
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, 19: keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 20: 0LtryCatch(parallel::mclapply(values, worker, mc.cores = cores, else 2L mc.preschedule = TRUE), error = function(e) NULL) }, output_handler = knit_handlers(options$render, options))
21: 40: SweepApply(theta, worker, numProcess)in_dir(input_dir(), expr)
22: 41: unlist(SweepApply(theta, worker, numProcess))in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 23: keep_message = if (is.numeric(options$message)) TRUE else options$message, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", stop_on_error = if (is.numeric(options$error)) options$error else { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (options$error && options$include) E = E, showPlot = TRUE) 0L
else 2L24: }, output_handler = knit_handlers(options$render, options)))eval(expr, envir)
42: 25: eng_r(options)eval(expr, envir)
43: 26: block_exec(params)withVisible(eval(expr, envir))
44: 27: call_block(x)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 45: { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) }process_group(group) if (on_message$silence) {
invokeRestart("muffleMessage") }46: }, warning = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (progress && is.function(pb$interrupt)) return() pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) })
if (on_warning$capture) {47: cnd <- sanitize_call(cnd)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { watcher$push(cnd) } if (progress && is.function(pb$interrupt)) if (on_warning$silence) { pb$interrupt() invokeRestart("muffleWarning") } if (is_R_CMD_build() || is_R_CMD_check()) }, error = function (cnd) { error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())) cnd <- sanitize_call(cnd)
watcher$push(cnd)48: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {})
if (progress && is.function(pb$interrupt)) 28: pb$interrupt()eval(call) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)29: }), list(rlang_trace_top_env = knit_global())), function(loc) {eval(call) setwd(wd)
write_utf8(res, output %n% stdout())30: paste0("\nQuitting from ", loc, if (!is.null(error)) with_handlers({ for (expr in tle$exprs) { paste0("\n", rule(), error, "\n", rule())) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }
TRUE49: }, handlers)process_file(text, output)
31: 50: doWithOneRestart(return(expr), restart)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
32: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withOneRestart(expr, restarts[[1L]]) output_dir = getwd(), ...)
52: 33: vweave_rmarkdown(...)
withRestartList(expr, restarts[-nr])53:
34: doWithOneRestart(return(expr), restart)engine$weave(file, quiet = quiet, encoding = enc)
35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])54: doTryCatch(return(expr), name, parentenv, handler)
36:
55: withRestartList(expr, restarts)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 56: withRestarts(with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))57: watcher$capture_plot_and_output()tryCatch({ watcher$print_value(ev$value, ev$visible, envir) engine$weave(file, quiet = quiet, encoding = enc) } setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 38: engine = engine)evaluate::evaluate(...) }
outputs <- c(outputs, output)39: }, error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, thisOK <<- FALSE keep_message = if (is.numeric(options$message)) TRUE else options$message, fails <<- c(fails, file) stop_on_error = if (is.numeric(options$error)) options$error else { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (options$error && options$include) file, conditionMessage(e))) 0L}) else 2L }, output_handler = knit_handlers(options$render, options))
58: 40: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", in_dir(input_dir(), expr) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp9A80f9/file8c0076e16a3a.rds")
41: An irrecoverable exception occurred. R is aborting now ...
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/Rtmp9A80f9/file8c0076e16a3a.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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/Rtmp9A80f9/file8c0076e16a3a.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