Last updated on 2026-08-05 09:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 2.94 | 223.19 | 226.13 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.56 | 218.38 | 220.94 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 358.17 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 186.14 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 131.00 | 136.00 | OK | |
| r-patched-linux-x86_64 | 1.15.4 | 136.52 | 67.86 | 204.38 | NOTE | |
| r-release-linux-x86_64 | 2.0.1 | 3.33 | 205.22 | 208.55 | 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 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 33.00 | 34.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 5.00 | 148.00 | 153.00 | OK |
Version: 1.15.4
Check: compiled code
Result: NOTE
File ‘rEDM/libs/rEDM.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Objects: ‘cppEDM/lib/libEDM.a’, ‘cppEDM/src/libEDM.a’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-patched-linux-x86_64
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
2026-08-05 16:07:23.819 R[46701:69769] 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:
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 1:
Traceback:
Traceback:
RowCumsum(valid) 1:
RowCumsum(valid) 2:
1: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, verbose = verbose)
RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 3: 3: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, verbose = verbose) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) tau = tau, theta = th, exclusionRadius = exclusionRadius, 3: embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
4: ComputeError(predictions$Observations, predictions$Predictions)
3: tau = tau, theta = th, exclusionRadius = exclusionRadius, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 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)$predictions)
6: FUN(X[[i]], ...) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 4: ComputeError(predictions$Observations, predictions$Predictions)
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: 7: ignoreNan = ignoreNan, backend = backend) 5: lapply(X = S, FUN = FUN, ...)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, lapply(X = S, FUN = FUN, ...)
4: ComputeError(predictions$Observations, predictions$Predictions)
8: doTryCatch(return(expr), name, parentenv, handler)
9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
8: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 10: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers) embedded = embedded, validLib = validLib, noTime = noTime,
11: tryCatch(expr, error = function(e) { embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
ignoreNan = ignoreNan, backend = backend)$predictions)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6:
FUN(X[[i]], ...)
7:
10: lapply(X = S, FUN = FUN, ...) 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { 8: call <- conditionCall(e)
8: doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) 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) call <- conditionCall(e) prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : " 9: msg <- paste0(prefix, conditionMessage(e), "\n") 9: if (!is.null(call)) { .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { if (identical(call[[1L]], quote(doTryCatch))) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
tryCatchOne(expr, names, parentenv, handlers[[1L]])12:
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) call <- sys.call(-4L)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) dcall <- deparse(call, nlines = 1L)
13: dcall <- deparse(call, nlines = 1L)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) prefix <- paste("Error in", dcall, ": ")tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")
14:
LONG <- 75LFUN(X[[i]], ...) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w))
15: 10: LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
lapply(seq_len(cores), inner.do)
16: 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler) type = "b") if (is.na(w)) if (!is.null(call)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
prefix <- paste0(prefix, "\n ") if (w > LONG) } 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"))) {19: } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") 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) cat(msg, file = outFile) .Internal(printDeferredWarnings()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) .Internal(seterrmessage(msg[1L])) }tryCatchList(expr, classes, parentenv, handlers) invisible(structure(msg, class = "try-error", condition = e))})
12:
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, try(lapply(X = S, FUN = FUN, ...), silent = TRUE)})
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) mc.preschedule = TRUE), error = function(e) NULL)
12:
if (!silent && isTRUE(getOption("show.error.messages"))) {21:
14: SweepApply(theta, worker, numProcess)
22: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: unlist(SweepApply(theta, worker, numProcess))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
23:
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", mc.preschedule = TRUE), error = function(e) NULL)
21:
SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 14: 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)
FUN(X[[i]], ...)17:
E = E, showPlot = TRUE)
15: 23: 24: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", eval(expr, envir) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26:
lapply(seq_len(cores), inner.do)
withVisible(eval(expr, envir))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)25:
doTryCatch(return(expr), name, parentenv, handler)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)27: withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)eval(expr, envir)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {
19: 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$push(cnd) } return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") } if (on_message$silence) { invokeRestart("muffleMessage") }21: tryCatchList(expr, classes, parentenv, handlers)}, error = function (cnd) SweepApply(theta, worker, numProcess)}, warning = function (cnd) {
22: unlist(SweepApply(theta, worker, numProcess)) watcher$capture_plot_and_output()
{
if (getOption("warn") >= 2 || getOption("warn") < 0) { return() cnd <- sanitize_call(cnd)20: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir) } watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
if (on_warning$capture) {
cnd <- sanitize_call(cnd)28: eval(call)
26: mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess) watcher$push(cnd) } if (on_warning$silence) {29: eval(call)
30: withVisible(eval(expr, envir)) invokeRestart("muffleWarning") }}, error = function (cnd) {with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 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) E = E, showPlot = TRUE)
watcher$print_value(ev$value, ev$visible, envir)24: 27: eval(expr, envir)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {})
28: eval(call) } watcher$push(cnd)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
29: eval(call)
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { TRUE}, handlers)
31: 30: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])with_handlers({
33: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: } watcher$push(cnd)withRestartList(expr, restarts[-nr]) if (on_message$silence) {withRestartList(expr, restarts[-nr]) }
invokeRestart("muffleMessage")34: doWithOneRestart(return(expr), restart) if (on_message$silence) { invokeRestart("muffleMessage")
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts) }}, warning = function (cnd) {
if (getOption("warn") >= 2 || getOption("warn") < 0) { }37: withRestarts(with_handlers({
34: return()doWithOneRestart(return(expr), restart)}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { for (expr in tle$exprs) { return() ev <- withVisible(eval(expr, envir)) } } watcher$capture_plot_and_output()
watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } watcher$capture_plot_and_output() if (on_warning$silence) { invokeRestart("muffleWarning")35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: watcher$print_value(ev$value, ev$visible, envir) if (on_warning$capture) { } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestarts(with_handlers({ stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { } if (options$error && options$include) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)42: eng_r(options) watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir)
43: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) }
28: eval(call)
29: eval(call)block_exec(params)
}30: if (on_warning$silence) { invokeRestart("muffleWarning") }with_handlers({
44: 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, call_block(x) for (expr in tle$exprs) { keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L
45: ev <- withVisible(eval(expr, envir))process_group(group)
46: }, output_handler = knit_handlers(options$render, options)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()32:
}, error = function (cnd) 40: { if (is_R_CMD_build() || is_R_CMD_check()) in_dir(input_dir(), expr) watcher$capture_plot_and_output()
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, withOneRestart(expr, restarts[[1L]]) stop_on_error = if (is.numeric(options$error)) options$error else {
33: withRestartList(expr, restarts[-nr]) if (options$error && options$include) cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) error <<- format(e)
0L else 2L34: })doWithOneRestart(return(expr), restart)
28: })eval(call) }, output_handler = knit_handlers(options$render, options)))
42: 47: eng_r(options)
43:
29: eval(call)
30:
with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEblock_exec(params)35:
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)}, handlers)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global())) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()31: doWithOneRestart(return(expr), restart)
if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])32: withOneRestart(expr, restarts[[1L]])48:
48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 36: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestartList(expr, restarts)withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: 37: error <<- format(e)call_block(x)
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {withRestarts(with_handlers({ }), list(rlang_trace_top_env = knit_global())), function(loc) {45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } setwd(wd) TRUE setwd(wd) error <<- format(e)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), write_utf8(res, output %n% stdout()) keep_message = if (is.numeric(options$message)) TRUE else options$message, paste0("\nQuitting from ", loc, if (!is.null(error)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) output_dir = getwd(), ...) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: 40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)52: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))process_file(text, output)
54: vweave_rmarkdown(...)
50:
42: eng_r(options)
43: block_exec(params)
44: doTryCatch(return(expr), name, parentenv, handler)call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()55: if (is_R_CMD_build() || is_R_CMD_check()) tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)53: engine$weave(file, quiet = quiet, encoding = enc)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }54:
outputs <- c(outputs, output) })doTryCatch(return(expr), name, parentenv, handler)
47: 51: }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (progress && is.function(pb$interrupt))
53: engine$weave(file, quiet = quiet, encoding = enc)
54: file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpODmM7B/file829b4396a525.rds")
An irrecoverable exception occurred. R is aborting now ...
pb$interrupt()
doTryCatch(return(expr), name, parentenv, handler) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: 56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) {tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) }), list(rlang_trace_top_env = knit_global())) thisOK <<- FALSE fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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$interrupt)) file, conditionMessage(e))) pb$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)) })
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/RtmpODmM7B/file829b4396a525.rds")
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) engine = engine)An irrecoverable exception occurred. R is aborting now ...
} 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/RtmpODmM7B/file829b4396a525.rds")
An irrecoverable exception occurred. R is aborting now ...
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpODmM7B/file829b4396a525.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