- using R version 4.5.2 Patched (2026-01-31 r89382)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.7.8
- using session charset: UTF-8
- checking for file ‘rEDM/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘rEDM’ version ‘2.0.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘rEDM’ can be installed ... [2s/2s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [2s/2s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [5s/2s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [18s/14s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-23 21:43:09.621 R[45069:69791] 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$render, options))
Traceback:
1: 40: RowCumsum(valid)in_dir(input_dir(), expr)
2: 41: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, in_input_dir(evaluate(code, envir = env, new_device = FALSE,
Traceback:
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 1: keep_message = if (is.numeric(options$message)) TRUE else options$message, RowCumsum(valid) tieBreak = FALSE, verbose = verbose)
stop_on_error = if (is.numeric(options$error)) options$error else {
2: if (options$error && options$include) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 3: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 0L tieBreak = FALSE, verbose = verbose) tau = tau, theta = th, exclusionRadius = exclusionRadius, else 2L
embedded = embedded, validLib = validLib, noTime = noTime, 3: }, output_handler = knit_handlers(options$render, options))) ignoreNan = ignoreNan, backend = backend)
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 4: 42: embedded = embedded, validLib = validLib, noTime = noTime, ComputeError(predictions$Observations, predictions$Predictions)eng_r(options)
5: ignoreNan = ignoreNan, backend = backend)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 4:
Traceback:
ComputeError(predictions$Observations, predictions$Predictions)43: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
1: embedded = embedded, validLib = validLib, noTime = noTime, 5: block_exec(params)RowCumsum(valid)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
2: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)$predictions)44: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, call_block(x) tieBreak = FALSE, verbose = verbose) ignoreNan = ignoreNan, backend = backend)$predictions)
45: process_group(group)
3: 6: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 6: FUN(X[[i]], ...)46: FUN(X[[i]], ...)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 7: tau = tau, theta = th, exclusionRadius = exclusionRadius, lapply(X = S, FUN = FUN, ...) error = function(e) {
embedded = embedded, validLib = validLib, noTime = noTime, if (progress && is.function(pb$interrupt)) 7: ignoreNan = ignoreNan, backend = backend) 8: lapply(X = S, FUN = FUN, ...)
pb$interrupt()
4: doTryCatch(return(expr), name, parentenv, handler)ComputeError(predictions$Observations, predictions$Predictions)
8: 5: if (is_R_CMD_build() || is_R_CMD_check()) 9: error <<- format(e)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, doTryCatch(return(expr), name, parentenv, handler) }) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)
9: 47: 10: 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchList(expr, classes, parentenv, handlers)10:
error = function(e) {
11: tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt)) tryCatch(expr, error = function(e) {
call <- conditionCall(e) pb$interrupt() 7: if (!is.null(call)) {11: lapply(X = S, FUN = FUN, ...)tryCatch(expr, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check())
call <- conditionCall(e) if (identical(call[[1L]], quote(doTryCatch))) 8: call <- sys.call(-4L) if (!is.null(call)) { error <<- format(e) dcall <- deparse(call, nlines = 1L)doTryCatch(return(expr), name, parentenv, handler) prefix <- paste("Error in", dcall, ": ") if (identical(call[[1L]], quote(doTryCatch))) }), list(rlang_trace_top_env = knit_global()))
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 9: call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")48: dcall <- deparse(call, nlines = 1L) if (is.na(w)) tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], LONG <- 75L
type = "b") sm <- strsplit(conditionMessage(e), "\n")[[1L]]10: if (w > LONG) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers) error = function(e) { prefix <- paste0(prefix, "\n ") if (is.na(w)) if (progress && is.function(pb$interrupt))
}11: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatch(expr, error = function(e) { type = "b") pb$interrupt() call <- conditionCall(e) if (w > LONG) else prefix <- "Error : " if (is_R_CMD_build() || is_R_CMD_check()) prefix <- paste0(prefix, "\n ") msg <- paste0(prefix, conditionMessage(e), "\n") } error <<- format(e) .Internal(seterrmessage(msg[1L])) }), list(rlang_trace_top_env = knit_global())), function(loc) { if (!silent && isTRUE(getOption("show.error.messages"))) { if (!is.null(call)) { setwd(wd) if (identical(call[[1L]], quote(doTryCatch))) cat(msg, file = outFile) call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) .Internal(printDeferredWarnings()) write_utf8(res, output %n% stdout()) prefix <- paste("Error in", dcall, ": ") } msg <- paste0(prefix, conditionMessage(e), "\n") invisible(structure(msg, class = "try-error", condition = e)) LONG <- 75L}) .Internal(seterrmessage(msg[1L])) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")12: cat(msg, file = outFile) if (is.na(w)) .Internal(printDeferredWarnings())try(lapply(X = S, FUN = FUN, ...), silent = TRUE) } paste0("\nQuitting from ", loc, if (!is.null(error)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
paste0("\n", rule(), error, "\n", rule())) type = "b") invisible(structure(msg, class = "try-error", condition = e))13: if (w > LONG) })}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) prefix <- paste0(prefix, "\n ")
49: 14: }process_file(text, output)
FUN(X[[i]], ...) else prefix <- "Error : "
50: 13:
msg <- paste0(prefix, conditionMessage(e), "\n")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))15:
lapply(seq_len(cores), inner.do)14: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)FUN(X[[i]], ...)
.Internal(seterrmessage(msg[1L]))16:
51: 15: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), lapply(seq_len(cores), inner.do) if (!silent && isTRUE(getOption("show.error.messages"))) {
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) output_dir = getwd(), ...) cat(msg, file = outFile)
16:
17: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)doTryCatch(return(expr), name, parentenv, handler) .Internal(printDeferredWarnings())
52: 17: }doTryCatch(return(expr), name, parentenv, handler)
vweave_rmarkdown(...)18: invisible(structure(msg, class = "try-error", condition = e))18: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 12: 19: 53: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)engine$weave(file, quiet = quiet, encoding = enc)
20: 54: 13: 20: doTryCatch(return(expr), name, parentenv, handler)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) mc.preschedule = TRUE), error = function(e) NULL)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))55: 21: 21: SweepApply(theta, worker, numProcess)
14: SweepApply(theta, worker, numProcess)
FUN(X[[i]], ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
22: unlist(SweepApply(theta, worker, numProcess))15: unlist(SweepApply(theta, worker, numProcess))
56: lapply(seq_len(cores), inner.do)23:
tryCatchList(expr, classes, parentenv, handlers)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 57: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 17: tryCatch({ E = E, showPlot = TRUE) E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler)
engine$weave(file, quiet = quiet, encoding = enc)
24: 24: 18: eval(expr, envir)eval(expr, envir) setwd(startdir)
tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "weave", engine = engine)
25: 19: 25: if (!have.makefile && vignette_is_tex(output)) {tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)eval(expr, envir) texi2pdf(file = output, clean = FALSE, quiet = quiet)
20: output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 26: 26: mc.preschedule = TRUE), error = function(e) NULL) }withVisible(eval(expr, envir)) outputs <- c(outputs, output)
27: 21: }, error = function(e) {withCallingHandlers(code, error = function (e) withVisible(eval(expr, envir)) thisOK <<- FALSESweepApply(theta, worker, numProcess)rlang::entrace(e), message = function (cnd)
fails <<- c(fails, file){ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 27: watcher$capture_plot_and_output() file, conditionMessage(e)))withCallingHandlers(code, error = function (e) 22: })rlang::entrace(e), message = function (cnd) unlist(SweepApply(theta, worker, numProcess)) if (on_message$capture) {{
watcher$push(cnd)23:
watcher$capture_plot_and_output() }58: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (on_message$capture) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (on_message$silence) { watcher$push(cnd)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", E = E, showPlot = TRUE) }
24: invokeRestart("muffleMessage") skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpQWxF7H/file9ee514cb01b8.rds")eval(expr, envir) }
if (on_message$silence) {An irrecoverable exception occurred. R is aborting now ...
}, warning = function (cnd) invokeRestart("muffleMessage"){ } if (getOption("warn") >= 2 || getOption("warn") < 0) {}, warning = function (cnd) {25: return() if (getOption("warn") >= 2 || getOption("warn") < 0) {eval(expr, envir) return()
} }26: withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$capture_plot_and_output()
if (on_warning$capture) {27: if (on_warning$capture) {withCallingHandlers(code, error = function (e) cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd)rlang::entrace(e), message = function (cnd) watcher$push(cnd) }{ if (on_warning$silence) { watcher$capture_plot_and_output() } invokeRestart("muffleWarning") if (on_warning$silence) { if (on_message$capture) { } watcher$push(cnd) invokeRestart("muffleWarning")}, error = function (cnd) }{ } watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)}, error = function (cnd) watcher$push(cnd){ switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() if (on_message$silence) { cnd <- sanitize_call(cnd) invokeRestart("muffleMessage") stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd) }})}, warning = function (cnd)
{ switch(on_error, continue = invokeRestart("eval_continue"), if (getOption("warn") >= 2 || getOption("warn") < 0) {28: return() stop = invokeRestart("eval_stop"), error = NULL)eval(call) }}) watcher$capture_plot_and_output()
29: if (on_warning$capture) {28: cnd <- sanitize_call(cnd)eval(call) watcher$push(cnd)eval(call) }
if (on_warning$silence) {
29: invokeRestart("muffleWarning")eval(call)30:
}with_handlers({30: }, error = function (cnd) with_handlers({{ for (expr in tle$exprs) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) cnd <- sanitize_call(cnd) watcher$capture_plot_and_output() watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir) switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() } stop = invokeRestart("eval_stop"), error = NULL) TRUE watcher$print_value(ev$value, ev$visible, envir) }}) TRUE
}, handlers)}, handlers)
28:
31: 31: eval(call)doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
32: 29: 32: withOneRestart(expr, restarts[[1L]])eval(call)withOneRestart(expr, restarts[[1L]])
30:
33: with_handlers({withRestartList(expr, restarts[-nr])33:
for (expr in tle$exprs) {34: ev <- withVisible(eval(expr, envir))withRestartList(expr, restarts[-nr])doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }
34: 36: TRUEwithRestartList(expr, restarts)}, handlers)doWithOneRestart(return(expr), restart)
35: 31: 37: doWithOneRestart(return(expr), restart)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withRestarts(with_handlers({
for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))32: watcher$capture_plot_and_output()36: watcher$print_value(ev$value, ev$visible, envir)withOneRestart(expr, restarts[[1L]])withRestartList(expr, restarts)
33: } TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)37: withRestartList(expr, restarts[-nr])
withRestarts(with_handlers({
38: 34: evaluate::evaluate(...) for (expr in tle$exprs) {doWithOneRestart(return(expr), restart) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()35: watcher$print_value(ev$value, ev$visible, envir)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])39: }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUE36: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
withRestartList(expr, restarts)38:
stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) evaluate::evaluate(...) 0L37:
else 2L39: withRestarts(with_handlers({ }, output_handler = knit_handlers(options$render, options)) for (expr in tle$exprs) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, ev <- withVisible(eval(expr, envir))
keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output()40: stop_on_error = if (is.numeric(options$error)) options$error else { watcher$print_value(ev$value, ev$visible, envir) if (options$error && options$include) in_dir(input_dir(), expr) } 0L TRUE
else 2L41: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }, output_handler = knit_handlers(options$render, options))in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 40: keep_message = if (is.numeric(options$message)) TRUE else options$message, in_dir(input_dir(), expr)38:
41: stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...) if (options$error && options$include) in_input_dir(evaluate(code, envir = env, new_device = FALSE, 0L keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
else 2L keep_message = if (is.numeric(options$message)) TRUE else options$message, 39: }, output_handler = knit_handlers(options$render, options))) stop_on_error = if (is.numeric(options$error)) options$error else {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 42: if (options$error && options$include) stop_on_error = if (is.numeric(options$error)) options$error else {eng_r(options) 0L
if (options$error && options$include) else 2L43: 0L }, output_handler = knit_handlers(options$render, options))) else 2Lblock_exec(params) }, output_handler = knit_handlers(options$render, options))
44:
42: call_block(x)40:
eng_r(options)in_dir(input_dir(), expr)
41: 45: 43: process_group(group)in_input_dir(evaluate(code, envir = env, new_device = FALSE, block_exec(params) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
44: keep_message = if (is.numeric(options$message)) TRUE else options$message, 46: stop_on_error = if (is.numeric(options$error)) options$error else {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (options$error && options$include) call_block(x) 0L error = function(e) {
else 2L45: if (progress && is.function(pb$interrupt)) process_group(group) pb$interrupt() }, output_handler = knit_handlers(options$render, options))) if (is_R_CMD_build() || is_R_CMD_check())
46: 42: error <<- format(e)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eng_r(options) })
43: error = function(e) {block_exec(params) if (progress && is.function(pb$interrupt))
pb$interrupt()47: if (is_R_CMD_build() || is_R_CMD_check()) 44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e)call_block(x) error = function(e) { })
if (progress && is.function(pb$interrupt)) 45: process_group(group)
pb$interrupt()
47: if (is_R_CMD_build() || is_R_CMD_check()) 46: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global())) error = function(e) { error = function(e) {
if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt()48: if (is_R_CMD_build() || is_R_CMD_check()) 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) { error <<- format(e) }), list(rlang_trace_top_env = knit_global())) if (progress && is.function(pb$interrupt)) })
pb$interrupt()48: 47: if (is_R_CMD_build() || is_R_CMD_check()) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() setwd(wd) 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)) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { }), list(rlang_trace_top_env = knit_global())) paste0("\n", rule(), error, "\n", rule())) setwd(wd)
write_utf8(res, output %n% stdout())}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)48: paste0("\nQuitting from ", loc, if (!is.null(error)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), paste0("\n", rule(), error, "\n", rule())) error = function(e) {
if (progress && is.function(pb$interrupt)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) pb$interrupt()49: if (is_R_CMD_build() || is_R_CMD_check())
process_file(text, output) error <<- format(e)49: process_file(text, output)
}), list(rlang_trace_top_env = knit_global())), function(loc) {50: setwd(wd)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) write_utf8(res, output %n% stdout())knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
paste0("\nQuitting from ", loc, if (!is.null(error)) 51: paste0("\n", rule(), error, "\n", rule()))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 51: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) output_dir = getwd(), ...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
49: process_file(text, output) output_dir = getwd(), ...)52:
50: vweave_rmarkdown(...)52: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)vweave_rmarkdown(...)
51: 53: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 53: output_dir = getwd(), ...)engine$weave(file, quiet = quiet, encoding = enc)engine$weave(file, quiet = quiet, encoding = enc)
52:
vweave_rmarkdown(...)54: 54: doTryCatch(return(expr), name, parentenv, handler)
53: doTryCatch(return(expr), name, parentenv, handler)55: engine$weave(file, quiet = quiet, encoding = enc)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 54: 55: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
56: 57: 55: tryCatchList(expr, classes, parentenv, handlers)tryCatch({tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)56: tryCatchList(expr, classes, parentenv, handlers) output <- find_vignette_product(name, by = "weave", engine = engine)57:
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) if (!have.makefile && vignette_is_tex(output)) { setwd(startdir) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "weave", engine = engine)57: output <- find_vignette_product(name, by = "texi2pdf", tryCatch({ if (!have.makefile && vignette_is_tex(output)) { engine = engine) texi2pdf(file = output, clean = FALSE, quiet = quiet) } output <- find_vignette_product(name, by = "texi2pdf", engine$weave(file, quiet = quiet, encoding = enc) outputs <- c(outputs, output) engine = engine)}, error = function(e) { setwd(startdir) } outputs <- c(outputs, output) output <- find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { thisOK <<- FALSE if (!have.makefile && vignette_is_tex(output)) { thisOK <<- FALSE fails <<- c(fails, file) texi2pdf(file = output, clean = FALSE, quiet = quiet) 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", output <- find_vignette_product(name, by = "texi2pdf", file, conditionMessage(e))) engine = engine) file, conditionMessage(e)))}) }
}) outputs <- c(outputs, output)
}, error = function(e) {58: 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", thisOK <<- FALSEtools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpQWxF7H/file9ee514cb01b8.rds") skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpQWxF7H/file9ee514cb01b8.rds") fails <<- c(fails, file)
An irrecoverable exception occurred. R is aborting now ...
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))An irrecoverable exception occurred. R is aborting now ...
})
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/RtmpQWxF7H/file9ee514cb01b8.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
- checking PDF version of manual ... [5s/5s] OK
- DONE
Status: 1 ERROR