Last updated on 2026-09-04 20:50:13 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.71 | 226.94 | 230.65 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.58 | 235.73 | 238.31 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.65 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 186.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 135.00 | 140.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.92 | 207.03 | 210.95 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.39 | 203.63 | 207.02 | 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 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 33.00 | 34.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 5.00 | 164.00 | 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
2026-09-04 10:51:09.431 R[47111:70168] 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)
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 6:
4: ComputeError(predictions$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]], ...)FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: 8: doTryCatch(return(expr), name, parentenv, handler)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))
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")10:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchList(expr, classes, parentenv, handlers) if (w > LONG) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) prefix <- paste0(prefix, "\n ") if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) tieBreak = FALSE, verbose = verbose) dcall <- deparse(call, nlines = 1L)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
type = "b")14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 4: ComputeError(predictions$Observations, predictions$Predictions)
mc.preschedule = TRUE), error = function(e) NULL) 5:
21: if (w > LONG) prefix <- paste0(prefix, "\n ")SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, } knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, E = E, showPlot = TRUE) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
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) {
Traceback:
cnd <- sanitize_call(cnd)}) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
watcher$push(cnd) }11: 13: if (on_warning$silence) { 1: RowCumsum(valid)
tryCatch(expr, error = function(e) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invokeRestart("muffleWarning") 2: call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")}, error = function (cnd) {14: LONG <- 75L validLib = validLib, libOverlap = idx$libOverlap, backend = backend, FUN(X[[i]], ...) tieBreak = FALSE, verbose = verbose) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
watcher$capture_plot_and_output()15: if (is.na(w))
cnd <- sanitize_call(cnd) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), 18: tau = tau, theta = th, exclusionRadius = exclusionRadius, stop = invokeRestart("eval_stop"), error = NULL)tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) embedded = embedded, validLib = validLib, noTime = noTime, type = "b")
ignoreNan = ignoreNan, backend = backend) if (w > LONG) prefix <- paste0(prefix, "\n ")20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
} mc.preschedule = TRUE), error = function(e) NULL)
21: 28: SweepApply(theta, worker, numProcess) 4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, eval(call)
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, else prefix <- "Error : " embedded = embedded, validLib = validLib, noTime = noTime,
22: 29: eval(call)unlist(SweepApply(theta, worker, numProcess))
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) ignoreNan = ignoreNan, backend = backend)$predictions)
if (!silent && isTRUE(getOption("show.error.messages"))) {23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: cat(msg, file = outFile)eval(expr, envir) }
TRUE
6: }, handlers) .Internal(printDeferredWarnings())FUN(X[[i]], ...)
25:
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: } invisible(structure(msg, class = "try-error", condition = e))}) 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
eval(expr, envir)
26: withVisible(eval(expr, envir))
27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) withRestartList(expr, restarts) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: withRestarts(with_handlers({
10: tryCatchList(expr, classes, parentenv, handlers)
11: for (expr in tle$exprs) {tryCatch(expr, error = function(e) {{12: ev <- withVisible(eval(expr, envir)) call <- conditionCall(e) watcher$capture_plot_and_output()try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
watcher$print_value(ev$value, ev$visible, envir) } if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) watcher$capture_plot_and_output()13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) call <- sys.call(-4L)
if (on_message$capture) { 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], watcher$push(cnd) }14: if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { TRUEFUN(X[[i]], ...)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: type = "b")
evaluate::evaluate(...) if (w > LONG)
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 { 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)) if (options$error && options$include) })
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: if (getOption("warn") >= 2 || getOption("warn") < 0) {15: FUN(X[[i]], ...)
0L15: 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)
return()lapply(seq_len(cores), inner.do)22:
16: unlist(SweepApply(theta, worker, numProcess))
else 2Lparallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)23:
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", }, output_handler = knit_handlers(options$render, options))19: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) }tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
24: eval(expr, envir)
21: 25: eval(expr, envir)
26: withVisible(eval(expr, envir))40: watcher$capture_plot_and_output()in_dir(input_dir(), expr)
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {
if (on_warning$capture) { watcher$push(cnd)41: cnd <- sanitize_call(cnd)in_input_dir(evaluate(code, envir = env, new_device = FALSE, } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, {SweepApply(theta, worker, numProcess) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) {
{ watcher$capture_plot_and_output()22: cnd <- sanitize_call(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { return() if (options$error && options$include) 0L } else 2L }, output_handler = knit_handlers(options$render, options)))
watcher$capture_plot_and_output()unlist(SweepApply(theta, worker, numProcess))42: switch(on_error, continue = invokeRestart("eval_continue"), if (on_warning$capture) {eng_r(options)
43: block_exec(params)
44: call_block(x)
cnd <- sanitize_call(cnd)45: watcher$push(cnd)
stop = invokeRestart("eval_stop"), error = NULL) }process_group(group)23: if (on_warning$silence) {})
invokeRestart("muffleWarning") }28: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", eval(call)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)46: }, error = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), E = E, showPlot = TRUE)
32: withOneRestart(expr, restarts[[1L]]){
24: eval(expr, envir)
25: eval(expr, envir)33:
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) error = function(e) {rlang::entrace(e), message = function (cnd) if (progress && is.function(pb$interrupt)) pb$interrupt(){ watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
error <<- format(e)withRestartList(expr, restarts[-nr]) })
47: watcher$capture_plot_and_output()
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), 28: if (on_message$capture) { watcher$push(cnd) error = function(e) {34: if (progress && is.function(pb$interrupt)) eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) pb$interrupt() }doWithOneRestart(return(expr), restart)
35: if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
error <<- format(e)36: }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) if (on_message$silence) { } invokeRestart("muffleMessage") }}, warning = function (cnd) {withRestartList(expr, restarts)
write_utf8(res, output %n% stdout()) TRUE37: if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }}, handlers)
31: doWithOneRestart(return(expr), restart)withRestarts(with_handlers({ watcher$capture_plot_and_output() paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output) for (expr in tle$exprs) {
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() if (on_warning$capture) { watcher$print_value(ev$value, ev$visible, envir) cnd <- sanitize_call(cnd) watcher$push(cnd) }32: if (on_warning$silence) { invokeRestart("muffleWarning")withOneRestart(expr, restarts[[1L]])51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } TRUE } output_dir = getwd(), ...)
}, error = function (cnd)
{ watcher$capture_plot_and_output()}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)52:
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$visible, envir)vweave_rmarkdown(...) cnd <- sanitize_call(cnd)
} TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)38: evaluate::evaluate(...)
watcher$push(cnd)39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
38: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
53: keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)28: stop_on_error = if (is.numeric(options$error)) options$error else {eval(call)
29: eval(call)
30: evaluate::evaluate(...) if (options$error && options$include)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])with_handlers({39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, for (expr in tle$exprs) { keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) 0L output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } ev <- withVisible(eval(expr, envir)) outputs <- c(outputs, output) if (options$error && options$include) else 2L watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])}, error = function(e) { 0L
else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
33: thisOK <<- FALSE fails <<- c(fails, file)withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }, output_handler = knit_handlers(options$render, options))37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))})
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/RtmphgBAFK/file928b3869257a.rds")
An irrecoverable exception occurred. R is aborting now ...
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$render, options)))40: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }
42: eng_r(options) TRUEin_dir(input_dir(), expr)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)
43: 44: block_exec(params)
44: call_block(x)
45: process_group(group)
46: 38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), evaluate::evaluate(...)call_block(x) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
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()) 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) })47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: pb$interrupt() if (progress && is.function(pb$interrupt)) pb$interrupt()in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { if (is_R_CMD_build() || is_R_CMD_check()) if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) 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)
if (is_R_CMD_build() || is_R_CMD_check()) 49: 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)process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) write_utf8(res, output %n% stdout())
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: 43: engine$weave(file, quiet = quiet, encoding = enc)
54: block_exec(params)
44: call_block(x) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56:
tryCatchList(expr, classes, parentenv, handlers)45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
pb$interrupt()57: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch({
49: process_file(text, output)
50: engine$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/RtmphgBAFK/file928b3869257a.rds")
An irrecoverable exception occurred. R is aborting now ...
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 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(), ...)
output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }
56: tryCatchList(expr, classes, parentenv, handlers)
57: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmphgBAFK/file928b3869257a.rds")
An irrecoverable exception occurred. R is aborting now ...
tryCatch({ engine$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/RtmphgBAFK/file928b3869257a.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