Last updated on 2026-09-17 17:50:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.26 | 227.12 | 230.38 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.46 | 217.14 | 219.60 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.64 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.99 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 136.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.02 | 209.65 | 213.67 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.45 | 210.54 | 213.99 | 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 | 23.00 | 24.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 5.00 | 159.00 | 164.00 | 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
2026-09-18 00:59:08.440 R[61800:94727] 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],
Traceback:
1: RowCumsum(valid) type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")
Traceback:
1: RowCumsum(valid)
2: } 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:
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$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, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
Traceback:
6: 1: RowCumsum(valid)
FUN(X[[i]], ...) ignoreNan = ignoreNan, backend = backend)
7:
lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler) 4: ComputeError(predictions$Observations, predictions$Predictions)
2: 5: 15: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 9:
lapply(seq_len(cores), inner.do) 6: validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)FUN(X[[i]], ...)
17: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { 3: call <- conditionCall(e)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
19: tryCatchList(expr, classes, parentenv, handlers) 7: if (!is.null(call)) {lapply(X = S, FUN = FUN, ...) ignoreNan = ignoreNan, backend = backend) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) 4: ComputeError(predictions$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: 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
dcall <- deparse(call, nlines = 1L) 8: doTryCatch(return(expr), name, parentenv, handler) mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)FUN(X[[i]], ...)
22:
unlist(SweepApply(theta, worker, numProcess))
9: prefix <- paste("Error in", dcall, ": ")23: 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], PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 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]] 7: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", lapply(X = S, FUN = FUN, ...) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
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) { type = "b") E = E, showPlot = TRUE)
if (w > LONG) if (is.na(w)) 24: call <- conditionCall(e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")eval(expr, envir) 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]] prefix <- paste0(prefix, "\n ")
} w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))25: if (is.na(w)) eval(expr, envir)
if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) .Internal(seterrmessage(msg[1L]))26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { if (!silent && isTRUE(getOption("show.error.messages"))) {}) cat(msg, file = outFile) watcher$capture_plot_and_output() if (on_message$capture) { prefix <- paste0(prefix, "\n ") } watcher$push(cnd)
else prefix <- "Error : "12: .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
msg <- paste0(prefix, conditionMessage(e), "\n")12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 13: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))FUN(X[[i]], ...)})
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
12: } if (on_message$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$push(cnd)14: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)17:
16: if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)17:
doTryCatch(return(expr), name, parentenv, handler)22: unlist(SweepApply(theta, worker, numProcess))
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20:
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output() target = "Thrips_imaginis", lib = "1 73", pred = "1 73", cnd <- sanitize_call(cnd)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) E = E, showPlot = TRUE)14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: watcher$push(cnd)
21: 24: eval(expr, envir)
25: eval(expr, envir)
26: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)
})
22: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { 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"), 28: unlist(SweepApply(theta, worker, numProcess)) stop = invokeRestart("eval_stop"), error = NULL)
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)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {18: tryCatchOne(expr, names, parentenv, handlers[[1L]])})
28:
eval(call)eval(call)
29:
eval(call)
30: watcher$capture_plot_and_output()with_handlers({ for (expr in tle$exprs) { if (on_message$capture) {19: watcher$push(cnd)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: ev <- withVisible(eval(expr, envir))29: watcher$capture_plot_and_output()unlist(SweepApply(theta, worker, numProcess)) } watcher$print_value(ev$value, ev$visible, envir) if (on_message$silence) {eval(call) } invokeRestart("muffleMessage") }}, warning = function (cnd) {
TRUE30: }, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) {
31: doWithOneRestart(return(expr), restart)23: with_handlers({ return() for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
}
watcher$capture_plot_and_output()32: 31: if (on_warning$capture) {withOneRestart(expr, restarts[[1L]])doWithOneRestart(return(expr), restart) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }
}, error = function (cnd)
32: withOneRestart(expr, restarts[[1L]])33:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE){33: withRestartList(expr, restarts[-nr])
withRestartList(expr, restarts[-nr])
24: eval(expr, envir)34:
watcher$capture_plot_and_output()25: doWithOneRestart(return(expr), restart)
eval(expr, envir)
26: withVisible(eval(expr, envir))
cnd <- sanitize_call(cnd)
27: withCallingHandlers(code, error = function (e) 34: 35: doWithOneRestart(return(expr), restart)
35: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
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$visible, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() TRUEwithOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
}, handlers)36: withRestartList(expr, restarts)
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)31: 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: doWithOneRestart(return(expr), restart)evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
32: withOneRestart(expr, restarts[[1L]]) if (on_message$capture) {
33:
withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) {35: if (getOption("warn") >= 2 || getOption("warn") < 0) { keep_message = if (is.numeric(options$message)) TRUE else options$message, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) stop_on_error = if (is.numeric(options$error)) options$error else {38:
return()evaluate::evaluate(...)
if (options$error && options$include) 39: 36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } 0L stop_on_error = if (is.numeric(options$error)) options$error else { else 2L }, output_handler = knit_handlers(options$render, options))
40: if (on_warning$silence) { invokeRestart("muffleWarning") if (options$error && options$include) } 0L}, error = function (cnd) withRestartList(expr, restarts)
37: {withRestarts(with_handlers({ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) for (expr in tle$exprs) { else 2L switch(on_error, continue = invokeRestart("eval_continue"), ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL)}) watcher$print_value(ev$value, ev$visible, envir) }, output_handler = knit_handlers(options$render, options))in_dir(input_dir(), expr)
}28: eval(call) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
29: eval(call)
40: 30: with_handlers({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,
for (expr in tle$exprs) {38: 41: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_message = if (is.numeric(options$message)) TRUE else options$message, 33: stop_on_error = if (is.numeric(options$error)) options$error else {withRestartList(expr, restarts[-nr])evaluate::evaluate(...)
keep_warning = if (is.numeric(options$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:
34: if (options$error && options$include) doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() 0Leng_r(options) else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) watcher$print_value(ev$value, ev$visible, envir)
43: } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
block_exec(params)39: 38:
43: block_exec(params)
44: call_block(x)
45: process_group(group)
evaluate::evaluate(...)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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) keep_message = if (is.numeric(options$message)) TRUE else options$message,
39: 46: 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: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: error = function(e) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
if (progress && is.function(pb$interrupt)) 40: pb$interrupt()in_dir(input_dir(), expr)
if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) 41: 47: pb$interrupt()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) error <<- format(e) pb$interrupt()in_input_dir(evaluate(code, envir = env, new_device = FALSE, })
47: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { error <<- format(e) setwd(wd) }), list(rlang_trace_top_env = knit_global())) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {47: write_utf8(res, output %n% stdout())with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (options$error && options$include) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) paste0("\nQuitting from ", loc, if (!is.null(error)) 0L error <<- format(e) pb$interrupt() }), list(rlang_trace_top_env = knit_global())) if (is_R_CMD_build() || is_R_CMD_check()) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), else 2L
}, output_handler = knit_handlers(options$render, options))) error <<- format(e)
42: eng_r(options)
48: }), list(rlang_trace_top_env = knit_global())), function(loc) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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)
error = function(e) {43: block_exec(params)
44: call_block(x)
50: output_dir = getwd(), ...)45: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)process_group(group)
if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)46:
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 52: 52: vweave_rmarkdown(...) error = function(e) {vweave_rmarkdown(...)
53: if (progress && is.function(pb$interrupt)) engine$weave(file, quiet = quiet, encoding = enc)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: pb$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), tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) {
56: }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)tryCatchList(expr, classes, parentenv, handlers)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
if (progress && is.function(pb$interrupt)) texi2pdf(file = output, clean = FALSE, quiet = quiet)53:
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 57: tryCatch({ engine$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", output <- find_vignette_product(name, by = "texi2pdf", }), list(rlang_trace_top_env = knit_global())) engine = engine)
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() engine = engine) } if (is_R_CMD_build() || is_R_CMD_check()) outputs <- c(outputs, output)engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) }
55: }, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) outputs <- c(outputs, output) write_utf8(res, output %n% stdout())}, error = function(e) { thisOK <<- FALSE paste0("\nQuitting from ", loc, if (!is.null(error)) thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: paste0("\n", rule(), error, "\n", rule()))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp93dOBe/fileb0493b541965.rds")
An irrecoverable exception occurred. R is aborting now ...
fails <<- c(fails, file)
56: tryCatchList(expr, classes, parentenv, handlers)
57: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatch({ engine$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)
49: } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 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", process_file(text, output) file, conditionMessage(e)))}) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp93dOBe/fileb0493b541965.rds")
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/Rtmp93dOBe/fileb0493b541965.rds")
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
An irrecoverable exception occurred. R is aborting now ...
51:
An irrecoverable exception occurred. R is aborting now ...
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/Rtmp93dOBe/fileb0493b541965.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