Last updated on 2026-09-12 19:50:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.43 | 222.55 | 225.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.73 | 235.84 | 238.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 177.28 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 184.77 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 136.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.64 | 210.51 | 214.15 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.44 | 203.68 | 207.12 | 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 | 131.00 | 137.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 130.00 | 131.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 163.00 | 170.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-13 02:57:33.852 R[47103:70702] 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)
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
4: ComputeError(predictions$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)
24: eval(expr, envir)
.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: 25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: 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]])
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")19: tryCatchList(expr, classes, parentenv, handlers)
}}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
} 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$capture_plot_and_output() cnd <- sanitize_call(cnd)21: SweepApply(theta, worker, numProcess)
22: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
28: eval(call)
29: eval(call)
30: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEwithVisible(eval(expr, envir))
Traceback:
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {}, handlers)
31: watcher$capture_plot_and_output() if (on_message$capture) {doWithOneRestart(return(expr), restart) watcher$push(cnd)
Traceback:
} 1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
32: withOneRestart(expr, restarts[[1L]])
1: if (on_message$silence) { invokeRestart("muffleMessage")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({ 3: RowCumsum(valid) for (expr in tle$exprs) {
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ev <- withVisible(eval(expr, envir)) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, } 2: }, warning = function (cnd) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
{ 3: watcher$capture_plot_and_output()
4: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, watcher$print_value(ev$value, ev$visible, envir) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
ComputeError(predictions$Observations, predictions$Predictions)
if (getOption("warn") >= 2 || getOption("warn") < 0) { 5: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, return() }SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)38: ignoreNan = ignoreNan, backend = backend)$predictions)
6: }evaluate::evaluate(...)
39:
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
watcher$capture_plot_and_output() 8: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L
else 2L 7: 9: lapply(X = S, FUN = FUN, ...) if (on_warning$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)tryCatchOne(expr, names, parentenv, handlers[[1L]])
}, output_handler = knit_handlers(options$render, options))
40:
in_dir(input_dir(), expr)10: tryCatchList(expr, classes, parentenv, handlers)
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 8: 11: doTryCatch(return(expr), name, parentenv, handler) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L30: if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: with_handlers({ for (expr in tle$exprs) { }, output_handler = knit_handlers(options$render, options))) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
tryCatchList(expr, classes, parentenv, handlers)42:
11: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") watcher$print_value(ev$value, ev$visible, envir) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eng_r(options)
43: type = "b")tryCatch(expr, error = function(e) { if (w > LONG) call <- conditionCall(e) TRUEblock_exec(params) 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))}) prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : "12: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))44: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)})call_block(x)
}, handlers)
31: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
45: process_group(group)
doWithOneRestart(return(expr), restart)14: 46: FUN(X[[i]], ...)
14: FUN(X[[i]], ...)
15: 15: lapply(seq_len(cores), inner.do)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)
16: 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
32: 21: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
SweepApply(theta, worker, numProcess)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()
withOneRestart(expr, restarts[[1L]])22:
17: if (is_R_CMD_build() || is_R_CMD_check()) unlist(SweepApply(theta, worker, numProcess))doTryCatch(return(expr), name, parentenv, handler)
error <<- format(e) })23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)33:
withRestartList(expr, restarts[-nr])18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)47: 25: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()34:
if (is_R_CMD_build() || is_R_CMD_check()) 21: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) SweepApply(theta, worker, numProcess)
22: watcher$capture_plot_and_output()unlist(SweepApply(theta, worker, numProcess))
if (on_message$capture) {doWithOneRestart(return(expr), restart) watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { paste0("\n", rule(), error, "\n", rule()))23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", return()35: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) } E = E, showPlot = TRUE) watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)
watcher$push(cnd)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24: eval(expr, envir)
} if (on_warning$silence) { invokeRestart("muffleWarning") }49:
36: withRestartList(expr, restarts)
}, error = function (cnd) 37: {process_file(text, output)25:
eval(expr, envir)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output()26: withVisible(eval(expr, envir))
27: cnd <- sanitize_call(cnd) watcher$push(cnd)withCallingHandlers(code, error = function (e) output_dir = getwd(), ...)
52: vweave_rmarkdown(...)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) {
53: }engine$weave(file, quiet = quiet, encoding = enc) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)
TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
if (getOption("warn") >= 2 || getOption("warn") < 0) {38: })
return()28: }evaluate::evaluate(...)54: doTryCatch(return(expr), name, parentenv, handler)eval(call)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: watcher$capture_plot_and_output()
39: tryCatchList(expr, classes, parentenv, handlers)29:
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (on_warning$capture) { engine = engine) }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE keep_message = if (is.numeric(options$message)) TRUE else options$message, cnd <- sanitize_call(cnd) } watcher$push(cnd) fails <<- c(fails, file) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (on_warning$silence) { file, conditionMessage(e))) TRUE})
stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers)
31: doWithOneRestart(return(expr), restart)
if (options$error && options$include) 32: invokeRestart("muffleWarning") 0LwithOneRestart(expr, restarts[[1L]])
33: else 2L }withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
}, output_handler = knit_handlers(options$render, options))35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
}, error = function (cnd)
36: withRestartList(expr, restarts)
58: {40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 37: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", keep_message = if (is.numeric(options$message)) TRUE else options$message, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpxHrMTC/file93d27bd648cc.rds") watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { cnd <- sanitize_call(cnd) if (options$error && options$include) withRestarts(with_handlers({ for (expr in tle$exprs) { watcher$push(cnd)
0L ev <- withVisible(eval(expr, envir))An irrecoverable exception occurred. R is aborting now ...
else 2L }, output_handler = knit_handlers(options$render, options)))
42: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }
28: 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, eval(call) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
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$visible, envir) 0L } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
else 2Leng_r(options)
43: block_exec(params)
44: call_block(x)
45: 32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {doWithOneRestart(return(expr), restart) if (progress && is.function(pb$interrupt)) }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: in_input_dir(evaluate(code, envir = env, new_device = FALSE, with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 35: error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L }), list(rlang_trace_top_env = knit_global())) else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
36: withRestartList(expr, restarts)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 37: withRestarts(with_handlers({ pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout())44: call_block(x)
45: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) paste0("\nQuitting from ", loc, if (!is.null(error)) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) paste0("\n", rule(), error, "\n", rule())) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })}, 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: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...) 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
53: engine$weave(file, quiet = quiet, encoding = enc)
else 2L }, output_handler = knit_handlers(options$render, options))54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)40: } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE error = function(e) { fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpxHrMTC/file93d27bd648cc.rds")
An irrecoverable exception occurred. R is aborting now ...
if (progress && is.function(pb$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 (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
45: process_group(group)
46: }), 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: 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()))
process_file(text, output)
50: 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()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 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())
52: vweave_rmarkdown(...) 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)
53: engine$weave(file, quiet = quiet, encoding = enc)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)57: tryCatch({ engine$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)}, 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/RtmpxHrMTC/file93d27bd648cc.rds") 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/RtmpxHrMTC/file93d27bd648cc.rds")
An irrecoverable exception occurred. R is aborting now ...
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