Last updated on 2026-08-14 01:51:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | OK | |||||
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.58 | 227.15 | 229.73 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 4.00 | 257.00 | 261.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.45 | 205.25 | 208.70 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 41.00 | 42.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 8.00 | 165.00 | 173.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-14 08:43:45.596 R[41454:60325] 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)
Traceback:
1: RowCumsum(valid)
2: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
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)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: ComputeError(predictions$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]], ...)
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))
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
14: 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, ": ")FUN(X[[i]], ...)
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))
Traceback:
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)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)
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 18: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
18:
19: tryCatchList(expr, classes, parentenv, handlers) 1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 21: embedded = embedded, validLib = validLib, noTime = noTime, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess)) ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...) mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: 7: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24:
23: eval(expr, envir)
Traceback:
1: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 25: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", eval(expr, envir)RowCumsum(valid) E = E, showPlot = TRUE)lapply(X = S, FUN = FUN, ...)
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)
{ 8: 26: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])withVisible(eval(expr, envir))
if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() 2: if (on_warning$capture) {
cnd <- sanitize_call(cnd)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, watcher$push(cnd) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: 10: tryCatchList(expr, classes, parentenv, handlers)
11: 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) }SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (on_warning$silence) {tryCatch(expr, error = function(e) { tau = tau, theta = th, exclusionRadius = exclusionRadius, } if (on_warning$silence) { invokeRestart("muffleWarning") call <- conditionCall(e) if (!is.null(call)) { }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) invokeRestart("muffleWarning") embedded = embedded, validLib = validLib, noTime = noTime, }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)with_handlers({
for (expr in tle$exprs) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") switch(on_error, continue = invokeRestart("eval_continue"), 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL) watcher$print_value(ev$value, ev$visible, envir)}) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...) }
LONG <- 75L28: eval(call)
29: 8: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler)
ev <- withVisible(eval(expr, envir)) TRUE watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)}, handlers) 9:
}31: tryCatchOne(expr, names, parentenv, handlers[[1L]]) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") TRUEdoWithOneRestart(return(expr), restart)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
if (is.na(w)) 10: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
tryCatchList(expr, classes, parentenv, handlers)
11:
tryCatch(expr, error = function(e) { call <- conditionCall(e)32: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 38: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b")withOneRestart(expr, restarts[[1L]])
33: if (w > LONG) withRestartList(expr, restarts[-nr])
34: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doWithOneRestart(return(expr), restart)evaluate::evaluate(...)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (is.na(w)) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 12:
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() type = "b")try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: watcher$print_value(ev$value, ev$visible, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
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 (w > LONG) 0L else 2L }, output_handler = knit_handlers(options$render, options))
}
40: in_dir(input_dir(), expr) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " TRUE msg <- paste0(prefix, conditionMessage(e), "\n")}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
14: FUN(X[[i]], ...) .Internal(seterrmessage(msg[1L])) 0L41: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) }
else 2Lin_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, }, output_handler = knit_handlers(options$render, options))
40: stop_on_error = if (is.numeric(options$error)) options$error else {15: lapply(seq_len(cores), inner.do) invisible(structure(msg, class = "try-error", condition = e))in_dir(input_dir(), expr)
41: if (options$error && options$include) in_input_dir(evaluate(code, envir = env, new_device = FALSE, })
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 0L
stop_on_error = if (is.numeric(options$error)) options$error else {16: if (options$error && options$include) else 2L14: FUN(X[[i]], ...)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
0L else 2L15: }, output_handler = knit_handlers(options$render, options)))
42:
}, output_handler = knit_handlers(options$render, options)))
eng_r(options)42: 17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)lapply(seq_len(cores), inner.do)
eng_r(options)
20: 43:
16: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, block_exec(params)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
mc.preschedule = TRUE), error = function(e) NULL)
43: 21: block_exec(params)SweepApply(theta, worker, numProcess)44: call_block(x)
44: call_block(x)
45: process_group(group)
18:
22: 45: 46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", unlist(SweepApply(theta, worker, numProcess)) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) process_group(group) E = E, showPlot = TRUE)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (is_R_CMD_build() || is_R_CMD_check()) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 24: error <<- format(e)eval(expr, envir) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {25: if (progress && is.function(pb$interrupt)) E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)eval(expr, envir) pb$interrupt()
26: if (is_R_CMD_build() || is_R_CMD_check()) withVisible(eval(expr, envir)) 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 <<- format(e) })
26: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {
27: error <<- format(e) pb$interrupt()withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) }), list(rlang_trace_top_env = knit_global())), function(loc) {{ watcher$capture_plot_and_output() setwd(wd) watcher$push(cnd) if (on_message$capture) { write_utf8(res, output %n% stdout()) } paste0("\nQuitting from ", loc, if (!is.null(error)) if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { watcher$push(cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() paste0("\n", rule(), error, "\n", rule())) }
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
switch(on_error, continue = invokeRestart("eval_continue"), 49: stop = invokeRestart("eval_stop"), error = NULL)48: watcher$capture_plot_and_output()})
if (on_warning$capture) {process_file(text, output)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), cnd <- sanitize_call(cnd)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$push(cnd) error = function(e) { } if (progress && is.function(pb$interrupt)) pb$interrupt()28: if (is_R_CMD_build() || is_R_CMD_check()) if (on_warning$silence) {eval(call)
invokeRestart("muffleWarning")
51: }rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { setwd(wd)
write_utf8(res, output %n% stdout())52: vweave_rmarkdown(...) ev <- withVisible(eval(expr, envir)) paste0("\nQuitting from ", loc, if (!is.null(error)) }, error = function (cnd)
53: watcher$capture_plot_and_output() paste0("\n", rule(), error, "\n", rule())){engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49:
} TRUEprocess_file(text, output)}, handlers)
31: doWithOneRestart(return(expr), restart)
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)32: 54: 50: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: doWithOneRestart(return(expr), restart)vweave_rmarkdown(...)doTryCatch(return(expr), name, parentenv, handler)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)29:
35: 55: eval(call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)30: if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])with_handlers({ for (expr in tle$exprs) { 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", ev <- withVisible(eval(expr, envir)) 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))) watcher$capture_plot_and_output()})
58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyihCJN/file6b2751eb1540.rds")
An irrecoverable exception occurred. R is aborting now ...
engine = engine)36: watcher$print_value(ev$value, ev$visible, envir) }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$visible, envir) outputs <- c(outputs, output) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39:
}, error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
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$exprs) {40: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE thisOK <<- FALSEin_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyihCJN/file6b2751eb1540.rds") keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0LAn irrecoverable exception occurred. R is aborting now ...
else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43:
42: eng_r(options)
43: block_exec(params)
44: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
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: 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: 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$weave(file, quiet = quiet, encoding = enc)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)54: doTryCatch(return(expr), name, parentenv, handler)
55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53:
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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)engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyihCJN/file6b2751eb1540.rds")
An irrecoverable exception occurred. R is aborting now ...
tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/RtmpyihCJN/file6b2751eb1540.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