Last updated on 2026-10-26 16:51:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.91 | 223.80 | 227.71 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.60 | 237.04 | 239.64 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.75 | 212.15 | 215.90 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.10 | 211.40 | 214.50 | 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 | 129.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 161.00 | 169.00 | 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
2026-10-26 23:11:41.218 R[45548:67981] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$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)))
Traceback:
1: })
RowCumsum(valid)
2: 58: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo12K5h/file90303d2588ec.rds")
An irrecoverable exception occurred. R is aborting now ...
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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))
Traceback:
23: 1: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", RowCumsum(valid) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, E = E, showPlot = TRUE)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)24:
eval(expr, envir) 3:
25: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, eval(expr, envir)
26: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, withVisible(eval(expr, envir)) ignoreNan = ignoreNan, backend = backend)
27: 4: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) ComputeError(predictions$Observations, predictions$Predictions){
5: watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (on_message$capture) { watcher$push(cnd) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) }
6: if (on_message$silence) {FUN(X[[i]], ...) invokeRestart("muffleMessage")
} 7: }, warning = function (cnd) {lapply(X = S, FUN = FUN, ...) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return() 8: }doTryCatch(return(expr), name, parentenv, handler)
watcher$capture_plot_and_output() if (on_warning$capture) { 9: cnd <- sanitize_call(cnd) watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
if (on_warning$silence) {10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { invokeRestart("muffleWarning") call <- conditionCall(e) } if (!is.null(call)) {}, error = function (cnd) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L){ dcall <- deparse(call, nlines = 1L) watcher$capture_plot_and_output() prefix <- paste("Error in", dcall, ": ") cnd <- sanitize_call(cnd) LONG <- 75L watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), sm <- strsplit(conditionMessage(e), "\n")[[1L]] stop = invokeRestart("eval_stop"), error = NULL) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")})
if (is.na(w)) 28: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(call) type = "b")
if (w > LONG) 29: eval(call) prefix <- paste0(prefix, "\n ") }
30: else prefix <- "Error : "with_handlers({ msg <- paste0(prefix, conditionMessage(e), "\n") for (expr in tle$exprs) { .Internal(seterrmessage(msg[1L])) ev <- withVisible(eval(expr, envir)) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) watcher$print_value(ev$value, ev$visible, envir) } } invisible(structure(msg, class = "try-error", condition = e)) TRUE})
}, handlers)
12: 31: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
doWithOneRestart(return(expr), restart)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))32:
withOneRestart(expr, restarts[[1L]])14:
Traceback:
FUN(X[[i]], ...)
1: 33: 15: withRestartList(expr, restarts[-nr])RowCumsum(valid)
lapply(seq_len(cores), inner.do) 2: 34:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, doWithOneRestart(return(expr), restart)
16: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 35: tieBreak = FALSE, verbose = verbose)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
36: withRestartList(expr, restarts) 3:
17: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, doTryCatch(return(expr), name, parentenv, handler)37:
tau = tau, theta = th, exclusionRadius = exclusionRadius, withRestarts(with_handlers({ embedded = embedded, validLib = validLib, noTime = noTime, 18: for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir))
ignoreNan = ignoreNan, backend = backend) watcher$capture_plot_and_output()
19: 4: tryCatchList(expr, classes, parentenv, handlers) watcher$print_value(ev$value, ev$visible, envir)
ComputeError(predictions$Observations, predictions$Predictions)
}20: 5: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)38: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
evaluate::evaluate(...)21:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 39: SweepApply(theta, worker, numProcess) embedded = embedded, validLib = validLib, noTime = noTime,
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 22: unlist(SweepApply(theta, worker, numProcess)) ignoreNan = ignoreNan, backend = backend)$predictions) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { 6: if (options$error && options$include) 23: FUN(X[[i]], ...) 0LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 7: lapply(X = S, FUN = FUN, ...) E = E, showPlot = TRUE) else 2L
8:
}, output_handler = knit_handlers(options$render, options))doTryCatch(return(expr), name, parentenv, handler)24:
eval(expr, envir)
9: 40: tryCatchOne(expr, names, parentenv, handlers[[1L]])25:
in_dir(input_dir(), expr)10:
eval(expr, envir)
tryCatchList(expr, classes, parentenv, handlers)26: withVisible(eval(expr, envir))41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 27: keep_message = if (is.numeric(options$message)) TRUE else options$message, 11: withCallingHandlers(code, error = function (e) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) rlang::entrace(e), message = function (cnd) 0L{ else 2L }, output_handler = knit_handlers(options$render, options)))
watcher$capture_plot_and_output() if (on_message$capture) {tryCatch(expr, error = function(e) { watcher$push(cnd)42: } if (on_message$silence) {eng_r(options) invokeRestart("muffleMessage") call <- conditionCall(e) if (!is.null(call)) { }
if (identical(call[[1L]], quote(doTryCatch))) }, warning = function (cnd) 43: block_exec(params){ call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) if (getOption("warn") >= 2 || getOption("warn") < 0) {44: prefix <- paste("Error in", dcall, ": ") return() LONG <- 75Lcall_block(x) } sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")45: process_group(group) if (is.na(w)) watcher$capture_plot_and_output()
if (on_warning$capture) { cnd <- sanitize_call(cnd) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 46: type = "b") watcher$push(cnd) if (w > LONG) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), prefix <- paste0(prefix, "\n ") error = function(e) { } } if (progress && is.function(pb$interrupt)) else prefix <- "Error : " pb$interrupt() if (on_warning$silence) { msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) if (is_R_CMD_build() || is_R_CMD_check()) invokeRestart("muffleWarning") error <<- format(e) } .Internal(printDeferredWarnings()) })
}, error = function (cnd) { } invisible(structure(msg, class = "try-error", condition = e))47: }) watcher$capture_plot_and_output()
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), cnd <- sanitize_call(cnd)12: error = function(e) { watcher$push(cnd)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) switch(on_error, continue = invokeRestart("eval_continue"), if (progress && is.function(pb$interrupt))
stop = invokeRestart("eval_stop"), error = NULL)})13: pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 28: error <<- format(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}), list(rlang_trace_top_env = knit_global()))eval(call)
14:
FUN(X[[i]], ...)48: 29: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(call)
error = function(e) { if (progress && is.function(pb$interrupt)) 15:
30: pb$interrupt()with_handlers({lapply(seq_len(cores), inner.do) for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check())
16: ev <- withVisible(eval(expr, envir)) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$capture_plot_and_output() setwd(wd)
watcher$print_value(ev$value, ev$visible, envir) write_utf8(res, output %n% stdout())17: paste0("\nQuitting from ", loc, if (!is.null(error)) doTryCatch(return(expr), name, parentenv, handler) } paste0("\n", rule(), error, "\n", rule()))
18: TRUE}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: 19: 49: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)process_file(text, output)
32: withOneRestart(expr, restarts[[1L]])21:
SweepApply(theta, worker, numProcess)
50: 33:
withRestartList(expr, restarts[-nr])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
22:
51: 34: unlist(SweepApply(theta, worker, numProcess))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
doWithOneRestart(return(expr), restart)23: output_dir = getwd(), ...)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 35: E = E, showPlot = TRUE)52:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])vweave_rmarkdown(...)24:
53: eval(expr, envir)36: engine$weave(file, quiet = quiet, encoding = enc)withRestartList(expr, restarts)
37:
withRestarts(with_handlers({54: 25: for (expr in tle$exprs) {eval(expr, envir)doTryCatch(return(expr), name, parentenv, handler)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()26: 55: watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }withVisible(eval(expr, envir)) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)56: 27:
withCallingHandlers(code, error = function (e) tryCatchList(expr, classes, parentenv, handlers)rlang::entrace(e), message = function (cnd) 38:
{evaluate::evaluate(...) watcher$capture_plot_and_output()
39: if (on_message$capture) {57: tryCatch({evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) } stop_on_error = if (is.numeric(options$error)) options$error else { if (on_message$silence) { setwd(startdir) if (options$error && options$include) 0L output <- find_vignette_product(name, by = "weave", engine = engine) invokeRestart("muffleMessage") else 2L } if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) }, output_handler = knit_handlers(options$render, options))}, warning = function (cnd) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)
40: {in_dir(input_dir(), expr) }
if (getOption("warn") >= 2 || getOption("warn") < 0) { outputs <- c(outputs, output) return()}, error = function(e) { }41: thisOK <<- FALSE watcher$capture_plot_and_output() if (on_warning$capture) { fails <<- c(fails, file)in_input_dir(evaluate(code, envir = env, new_device = FALSE, cnd <- sanitize_call(cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd) file, conditionMessage(e))) stop_on_error = if (is.numeric(options$error)) options$error else {}) } if (on_warning$silence) {
if (options$error && options$include) invokeRestart("muffleWarning")58: 0Ltools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", else 2L } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo12K5h/file90303d2588ec.rds") }, output_handler = knit_handlers(options$render, options)))}, error = function (cnd)
An irrecoverable exception occurred. R is aborting now ...
42: eng_r(options){
watcher$capture_plot_and_output()43: cnd <- sanitize_call(cnd)block_exec(params) watcher$push(cnd)
44: switch(on_error, continue = invokeRestart("eval_continue"), call_block(x)
stop = invokeRestart("eval_stop"), error = NULL)45: })process_group(group)
28: 46: eval(call)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
if (progress && is.function(pb$interrupt)) 29: pb$interrupt()eval(call) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)30: with_handlers({ })
47: for (expr in tle$exprs) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ev <- withVisible(eval(expr, envir)) error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) watcher$print_value(ev$value, ev$visible, envir) } pb$interrupt() TRUE}, handlers) if (is_R_CMD_build() || is_R_CMD_check())
31: error <<- format(e)doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]]) }), list(rlang_trace_top_env = knit_global()))
33:
withRestartList(expr, restarts[-nr])48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {34: if (progress && is.function(pb$interrupt)) doWithOneRestart(return(expr), restart) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)35: }), list(rlang_trace_top_env = knit_global())), function(loc) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) setwd(wd)
write_utf8(res, output %n% stdout())36: paste0("\nQuitting from ", loc, if (!is.null(error)) withRestartList(expr, restarts)
37: paste0("\n", rule(), error, "\n", rule()))withRestarts(with_handlers({}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))49: watcher$capture_plot_and_output()process_file(text, output)
50: watcher$print_value(ev$value, ev$visible, envir)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) } TRUE
51: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
52: 38: vweave_rmarkdown(...)evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 53: engine$weave(file, quiet = quiet, encoding = enc)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 54: stop_on_error = if (is.numeric(options$error)) options$error else {doTryCatch(return(expr), name, parentenv, handler)
if (options$error && options$include) 55: 0LtryCatchOne(expr, names, parentenv, handlers[[1L]])
else 2L56: }, output_handler = knit_handlers(options$render, options))tryCatchList(expr, classes, parentenv, handlers)
57:
tryCatch({40: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)in_dir(input_dir(), expr) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 41: engine = engine)in_input_dir(evaluate(code, envir = env, new_device = FALSE, } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, outputs <- c(outputs, output) keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function(e) { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L thisOK <<- FALSE fails <<- c(fails, file) }, output_handler = knit_handlers(options$render, options)))
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 42: eng_r(options) file, conditionMessage(e)))
})43: block_exec(params)
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
44: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo12K5h/file90303d2588ec.rds")call_block(x)
An irrecoverable exception occurred. R is aborting now ...
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo12K5h/file90303d2588ec.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