Last updated on 2026-10-27 05:58:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.91 | 223.80 | 227.71 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.69 | 239.81 | 242.50 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.75 | 212.15 | 215.90 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.10 | 211.40 | 214.50 | 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 | 129.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 40.00 | 42.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 161.00 | 169.00 | 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
2026-10-27 14:24:49.394 R[53449:83599] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
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) { 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"), 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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { 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: 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()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
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/RtmpSPOog1/filea83f1fdb6362.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
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) { 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"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30:
Traceback:
with_handlers({ 1: for (expr in tle$exprs) {RowCumsum(valid) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) } 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) TRUE}, handlers)
3: 31: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, doWithOneRestart(return(expr), restart) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)32:
withOneRestart(expr, restarts[[1L]]) 4:
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$exprs) { ev <- withVisible(eval(expr, envir)) watcher$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$include)
Traceback:
1: RowCumsum(valid) 0L
else 2L 2: }, output_handler = knit_handlers(options$render, options))FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 40: tieBreak = FALSE, verbose = verbose)in_dir(input_dir(), expr)
ComputeError(predictions$Observations, predictions$Predictions)
3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 5: 41: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, in_input_dir(evaluate(code, envir = env, new_device = FALSE, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)$predictions) embedded = embedded, validLib = validLib, noTime = noTime, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 6: stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend)FUN(X[[i]], ...) if (options$error && options$include)
4: 0L
else 2LComputeError(predictions$Observations, predictions$Predictions) }, output_handler = knit_handlers(options$render, options)))
5: 42: 7: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, lapply(X = S, FUN = FUN, ...)eng_r(options)
8: 43: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, block_exec(params) embedded = embedded, validLib = validLib, noTime = noTime,
doTryCatch(return(expr), name, parentenv, handler)
44: ignoreNan = ignoreNan, backend = backend)$predictions) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])call_block(x) 6:
FUN(X[[i]], ...)
10:
45: 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
process_group(group)tryCatchList(expr, classes, parentenv, handlers)
46: 11: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {tryCatch(expr, error = function(e) { call <- conditionCall(e) 9: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 10: error <<- format(e)tryCatchList(expr, classes, parentenv, handlers) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 11: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) tryCatch(expr, error = function(e) { error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: call <- conditionCall(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (!is.null(call)) { error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) if (progress && is.function(pb$interrupt)) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L pb$interrupt() sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is_R_CMD_build() || is_R_CMD_check()) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error <<- format(e) if (is.na(w)) }), list(rlang_trace_top_env = knit_global())), function(loc) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], setwd(wd) type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (w > LONG) if (is.na(w)) write_utf8(res, output %n% stdout()) prefix <- paste0(prefix, "\n ") paste0("\nQuitting from ", loc, if (!is.null(error)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } paste0("\n", rule(), error, "\n", rule())) else prefix <- "Error : "}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) type = "b") if (!silent && isTRUE(getOption("show.error.messages"))) { if (w > LONG) cat(msg, file = outFile) prefix <- paste0(prefix, "\n ")49: .Internal(printDeferredWarnings())process_file(text, output) } }
else prefix <- "Error : " invisible(structure(msg, class = "try-error", condition = e))}) msg <- paste0(prefix, conditionMessage(e), "\n")50:
12: .Internal(seterrmessage(msg[1L]))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)13: .Internal(printDeferredWarnings())sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
}
14: FUN(X[[i]], ...) invisible(structure(msg, class = "try-error", condition = e))
})15:
lapply(seq_len(cores), inner.do)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 17: output_dir = getwd(), ...)13:
doTryCatch(return(expr), name, parentenv, handler)52: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
vweave_rmarkdown(...)14: 18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...)53:
engine$weave(file, quiet = quiet, encoding = enc)
15:
19: lapply(seq_len(cores), inner.do)54: tryCatchList(expr, classes, parentenv, handlers)
doTryCatch(return(expr), name, parentenv, handler)20: 16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 55: mc.preschedule = TRUE), error = function(e) NULL)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: 21: 56: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess)tryCatchList(expr, classes, parentenv, handlers)
18: 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])57: unlist(SweepApply(theta, worker, numProcess))
19: tryCatch({23: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", tryCatchList(expr, classes, parentenv, handlers) output <- find_vignette_product(name, by = "weave", engine = engine) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
if (!have.makefile && vignette_is_tex(output)) {20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
E = E, showPlot = TRUE) texi2pdf(file = output, clean = FALSE, quiet = quiet)21: output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)SweepApply(theta, worker, numProcess)24:
}22: eval(expr, envir)unlist(SweepApply(theta, worker, numProcess))
25: outputs <- c(outputs, output)eval(expr, envir)}, error = function(e) {
26: withVisible(eval(expr, envir))
thisOK <<- FALSE27: fails <<- c(fails, file)23: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", withCallingHandlers(code, error = function (e) file, conditionMessage(e)))rlang::entrace(e), message = function (cnd) }){PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
watcher$capture_plot_and_output() target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (on_message$capture) { E = E, showPlot = TRUE) watcher$push(cnd)
58: }24: eval(expr, envir) if (on_message$silence) {
invokeRestart("muffleMessage")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 25: } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpSPOog1/filea83f1fdb6362.rds")}, warning = function (cnd) eval(expr, envir){
An irrecoverable exception occurred. R is aborting now ...
if (getOption("warn") >= 2 || getOption("warn") < 0) {26: return()withVisible(eval(expr, envir)) }
watcher$capture_plot_and_output()27: if (on_warning$capture) {withCallingHandlers(code, error = function (e) cnd <- sanitize_call(cnd)rlang::entrace(e), message = function (cnd) watcher$push(cnd) }{ if (on_warning$silence) { watcher$capture_plot_and_output() invokeRestart("muffleWarning") if (on_message$capture) { } watcher$push(cnd)}, error = function (cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return(){ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) } watcher$push(cnd) watcher$capture_plot_and_output() switch(on_error, continue = invokeRestart("eval_continue"), if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) stop = invokeRestart("eval_stop"), error = NULL)})
}28: if (on_warning$silence) {eval(call)
invokeRestart("muffleWarning")29: }eval(call)}, error = function (cnd)
{30: watcher$capture_plot_and_output()with_handlers({ for (expr in tle$exprs) { cnd <- sanitize_call(cnd) ev <- withVisible(eval(expr, envir)) watcher$push(cnd) watcher$capture_plot_and_output() switch(on_error, continue = invokeRestart("eval_continue"), watcher$print_value(ev$value, ev$visible, envir) stop = invokeRestart("eval_stop"), error = NULL) }})
TRUE}, handlers)28:
31: doWithOneRestart(return(expr), restart)eval(call)
32: withOneRestart(expr, restarts[[1L]])29: eval(call)
30: 33: with_handlers({withRestartList(expr, restarts[-nr]) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))34: watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart)
watcher$print_value(ev$value, ev$visible, envir) }35: TRUEwithOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])}, handlers)
36: 31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])withRestartList(expr, restarts)
34: 37: doWithOneRestart(return(expr), restart)withRestarts(with_handlers({
for (expr in tle$exprs) {35: ev <- withVisible(eval(expr, envir))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)36: } TRUEwithRestartList(expr, restarts)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
37: 38: withRestarts(with_handlers({evaluate::evaluate(...) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))39: watcher$capture_plot_and_output()evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$print_value(ev$value, ev$visible, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { TRUE if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
40: 38: in_dir(input_dir(), expr)evaluate::evaluate(...)
41: 39: in_input_dir(evaluate(code, envir = env, new_device = FALSE, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) if (options$error && options$include) 0L 0L else 2L }, output_handler = knit_handlers(options$render, options)) else 2L
}, output_handler = knit_handlers(options$render, options)))
40: 42: in_dir(input_dir(), expr)eng_r(options)
41: 43: in_input_dir(evaluate(code, envir = env, new_device = FALSE, block_exec(params) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 44: stop_on_error = if (is.numeric(options$error)) options$error else {call_block(x) if (options$error && options$include)
45: process_group(group) 0L
else 2L46: }, output_handler = knit_handlers(options$render, options)))
42: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eng_r(options)
error = function(e) {43: if (progress && is.function(pb$interrupt)) pb$interrupt()block_exec(params) if (is_R_CMD_build() || is_R_CMD_check())
44: call_block(x)
error <<- format(e)45: })process_group(group)
47: 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) if (is_R_CMD_build() || is_R_CMD_check())
47: error <<- format(e)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global())) error = function(e) {
48: if (progress && is.function(pb$interrupt)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())) pb$interrupt()
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error = function(e) { }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) write_utf8(res, output %n% stdout()) error <<- format(e) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 49: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)process_file(text, output)
49:
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 52: output_dir = getwd(), ...)vweave_rmarkdown(...)
53: 52: vweave_rmarkdown(...)engine$weave(file, quiet = quiet, encoding = enc)
53: 54: engine$weave(file, quiet = quiet, encoding = enc)doTryCatch(return(expr), name, parentenv, handler)
54: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
55: 56: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
56: tryCatchList(expr, classes, parentenv, handlers)
57: 57: tryCatch({tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } engine = engine) outputs <- c(outputs, output) }}, error = function(e) { outputs <- c(outputs, output) thisOK <<- FALSE}, error = function(e) { fails <<- c(fails, file) thisOK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", fails <<- c(fails, file) file, conditionMessage(e)))}) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
58: file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpSPOog1/filea83f1fdb6362.rds")
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpSPOog1/filea83f1fdb6362.rds")
An irrecoverable exception occurred. R is aborting now ...
An irrecoverable exception occurred. R is aborting now ...
Quitting from rEDM-tutorial.Rmd:466-469 [smap_thrips]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 15, 0
---
Backtrace:
▆
1. └─rEDM::PredictNonlinear(...)
2. └─base::data.frame(Theta = theta, rho = rho)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rEDM-tutorial.Rmd' failed with diagnostics:
arguments imply differing number of rows: 15, 0
--- failed re-building ‘rEDM-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘rEDM-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64