Last updated on 2026-08-31 02:51:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.45 | 222.09 | 225.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.45 | 228.69 | 231.14 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 183.45 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 182.49 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 132.00 | 137.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 3.38 | 211.41 | 214.79 | 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 | 2.0.1 | 7.00 | 137.00 | 144.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 28.00 | 29.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 164.00 | 172.00 | 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
2026-08-31 11:06:02.686 R[48409:71406] 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))
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: watcher$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()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)$predictions)
if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler) if (on_warning$silence) { invokeRestart("muffleWarning") }
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
}, error = function (cnd) { watcher$capture_plot_and_output()11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
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: 28: 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:
Traceback:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: eval(call) 1: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, RowCumsum(valid)
Traceback:
1: RowCumsum(valid)
29: 2: mc.preschedule = TRUE), error = function(e) NULL)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)eval(call)
2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 3: tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 21: ignoreNan = ignoreNan, backend = backend)
watcher$print_value(ev$value, ev$visible, envir) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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]], ...)SweepApply(theta, worker, numProcess) TRUE
4: ComputeError(predictions$Observations, predictions$Predictions)}, handlers)
22: 7: 31:
lapply(X = S, FUN = FUN, ...)doWithOneRestart(return(expr), restart) 5:
32: withOneRestart(expr, restarts[[1L]])unlist(SweepApply(theta, worker, numProcess))
33:
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)
withRestartList(expr, restarts[-nr])SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 26: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
8: doTryCatch(return(expr), name, parentenv, handler)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8:
doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {
10: tryCatchList(expr, classes, parentenv, handlers) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)27: 34: dcall <- deparse(call, nlines = 1L)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) prefix <- paste("Error in", dcall, ": "){ watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) }11: LONG <- 75L if (on_message$silence) { invokeRestart("muffleMessage") sm <- strsplit(conditionMessage(e), "\n")[[1L]]doWithOneRestart(return(expr), restart) }tryCatch(expr, error = function(e) {}, warning = function (cnd)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE){ if (getOption("warn") >= 2 || getOption("warn") < 0) { 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]] return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") if (is.na(w)) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) if (on_warning$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"), .Internal(seterrmessage(msg[1L])) 0L type = "b") if (!silent && isTRUE(getOption("show.error.messages"))) { stop = invokeRestart("eval_stop"), error = NULL)}) else 2L
if (w > LONG) 28: }, output_handler = knit_handlers(options$render, options))eval(call)
29: eval(call)
30: with_handlers({ prefix <- paste0(prefix, "\n ") }40: in_dir(input_dir(), expr) cat(msg, file = outFile)
for (expr in tle$exprs) { else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, ev <- withVisible(eval(expr, envir)) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
if (!silent && isTRUE(getOption("show.error.messages"))) { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L12: cat(msg, file = outFile) .Internal(printDeferredWarnings()) }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) watcher$print_value(ev$value, ev$visible, envir) } invisible(structure(msg, class = "try-error", condition = e)) TRUE})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
}, handlers)
43: block_exec(params)31:
44: 13: call_block(x)doWithOneRestart(return(expr), restart)
32: 13: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))doWithOneRestart(return(expr), restart)
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
14: error = function(e) {16: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
FUN(X[[i]], ...)
15: 47: 35: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])lapply(seq_len(cores), inner.do)
36: withRestartList(expr, restarts)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) error = function(e) { if (progress && is.function(pb$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))
17: doTryCatch(return(expr), name, parentenv, handler)
18: pb$interrupt()
37: withRestarts(with_handlers({ for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) 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: 19: 20: process_file(text, output)
tryCatchList(expr, classes, parentenv, handlers) 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)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)50: 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23:
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 38: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", mc.preschedule = TRUE), error = function(e) NULL) output_dir = getwd(), ...)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$render, options))
E = E, showPlot = TRUE)
24: 52: 40: vweave_rmarkdown(...)
53: 21: engine$weave(file, quiet = quiet, encoding = enc)
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) 0Leval(expr, envir)54: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
25: doTryCatch(return(expr), name, parentenv, handler)
else 2L23: 55: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tryCatchOne(expr, names, parentenv, handlers[[1L]]) 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$capture_plot_and_output()eval(expr, envir)
}, output_handler = knit_handlers(options$render, options)))
26: 56: if (on_message$capture) {withVisible(eval(expr, envir))
27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output()42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: watcher$push(cnd) if (on_message$capture) { } if (on_message$silence) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") error = function(e) {
} if (progress && is.function(pb$interrupt)) pb$interrupt()}, warning = function (cnd) invokeRestart("muffleMessage"){ }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (getOption("warn") >= 2 || getOption("warn") < 0) {57: return() } watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) return()tryCatch({ if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } watcher$capture_plot_and_output() } if (on_warning$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)
})
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine$weave(file, quiet = quiet, encoding = enc) if (on_warning$capture) {29: setwd(startdir) error = function(e) { 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", if (progress && is.function(pb$interrupt)) engine = engine) pb$interrupt() } outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) cnd <- sanitize_call(cnd) watcher$push(cnd) } error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
}, error = function(e) {eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() thisOK <<- FALSE watcher$print_value(ev$value, ev$visible, envir) if (on_warning$silence) { fails <<- c(fails, file) } TRUE}, handlers) invokeRestart("muffleWarning") }}, error = function (cnd) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
31: file, conditionMessage(e)))doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])48: })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpnwLhwH/file843f49b9e077.rds") watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
An irrecoverable exception occurred. R is aborting now ...
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)
paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))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 { stop = invokeRestart("eval_stop"), error = NULL) if (options$error && options$include) })}, 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$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
28: 0L else 2L }, output_handler = knit_handlers(options$render, options))eval(call)
29: eval(call)
57: 30:
with_handlers({40: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
in_dir(input_dir(), expr)31: doWithOneRestart(return(expr), restart)
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) }
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, 32: stop_on_error = if (is.numeric(options$error)) options$error else { outputs <- c(outputs, output)}, error = function(e) { if (options$error && options$include) withOneRestart(expr, restarts[[1L]]) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
33: withRestartList(expr, restarts[-nr]) thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
34: 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpnwLhwH/file843f49b9e077.rds")
An irrecoverable exception occurred. R is aborting now ...
doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) {
42: eng_r(options) 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:
43: block_exec(params)
44: 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, call_block(x)
45: process_group(group)
46: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))40: in_dir(input_dir(), expr)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
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()))42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: 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)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
}), 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)52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/RtmpnwLhwH/file843f49b9e077.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpnwLhwH/file843f49b9e077.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