Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-19 09:39:17.410 R[41443:60353] 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$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$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$message, 
Traceback:
 1: RowCumsum(valid)
 2:     stop_on_error = if (is.numeric(options$error)) options$error else {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,         if (options$error && options$include)             0L
Traceback:
        else 2L    validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
 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)$predictions)
 6:  1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, FUN(X[[i]], ...)    tau = tau, theta = th, exclusionRadius = exclusionRadius, 
 7:     }, output_handler = knit_handlers(options$render, options)))    embedded = embedded, validLib = validLib, noTime = noTime, 
42: eng_r(options)lapply(X = S, FUN = FUN, ...)
Traceback:

43: block_exec(params)
44: call_block(x)
45:     ignoreNan = ignoreNan, backend = backend)process_group(group)

 1: 46: 
RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  4: ComputeError(predictions$Observations, predictions$Predictions)
 5:  8: doTryCatch(return(expr), name, parentenv, handler)
    ignoreNan = ignoreNan, backend = backend)$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: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
47: tryCatchList(expr, classes, parentenv, handlers)
 9: 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, ": ")    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])    embedded = embedded, validLib = validLib, noTime = noTime,         LONG <- 75L    ignoreNan = ignoreNan, backend = backend)$predictions)        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w)) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))        if (w > LONG) 
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]            prefix <- paste0(prefix, "\n  ")48:     } 6: FUN(X[[i]], ...)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),         w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
 7: lapply(X = S, FUN = FUN, ...)    error = function(e) {
        if (progress && is.function(pb$interrupt))  8:             pb$interrupt()        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (is_R_CMD_build() || is_R_CMD_check()) doTryCatch(return(expr), name, parentenv, handler)        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    else prefix <- "Error : "    }            error <<- format(e)    msg <- paste0(prefix, conditionMessage(e), "\n")    else prefix <- "Error : "
    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    msg <- paste0(prefix, conditionMessage(e), "\n")    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(),     .Internal(seterrmessage(msg[1L]))    .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))})
    if (!silent && isTRUE(getOption("show.error.messages"))) {    output_dir = getwd(), ...) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14:         cat(msg, file = outFile)FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)

11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {52:         .Internal(printDeferredWarnings())        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")    }    invisible(structure(msg, class = "try-error", condition = e))})
        if (is.na(w)) 15: 12: lapply(seq_len(cores), inner.do)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)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: 13: 
16: tryCatchList(expr, classes, parentenv, handlers)            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 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)                type = "b")
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")17:     }doTryCatch(return(expr), name, parentenv, handler)

    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))18:     if (!silent && isTRUE(getOption("show.error.messages"))) {17: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])
57:         cat(msg, file = outFile)tryCatch({18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 
        .Internal(printDeferredWarnings())19:     }    invisible(structure(msg, class = "try-error", condition = e))})
12:     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)tryCatchList(expr, classes, parentenv, handlers)
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: 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)unlist(SweepApply(theta, worker, numProcess))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))

    }    outputs <- c(outputs, output)}, error = function(e) {23: 
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)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
        watcher$push(cnd)    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6ekfKA/file6b5171c3984a.rds")
An irrecoverable exception occurred. R is aborting now ...
    }    if (on_warning$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))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:         watcher$capture_plot_and_output()14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)        watcher$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$include)             0Leval(call)})
28: eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$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:         else 2L    }, output_handler = knit_handlers(options$render, options)))
42: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$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, 
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), 29:     error = function(e) {eval(call)    keep_message = if (is.numeric(options$message)) TRUE else options$message,         if (progress && is.function(pb$interrupt))     stop_on_error = if (is.numeric(options$error)) options$error else {
30: with_handlers({            pb$interrupt()    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        if (options$error && options$include)         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()))        watcher$print_value(ev$value, ev$visible, envir)            0L        else 2L    }, output_handler = knit_handlers(options$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$render, options)))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
    }
    TRUE49: process_file(text, output)
50: }, handlers)
42: eng_r(options)
43: block_exec(params)
44: 31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
            pb$interrupt()51:         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })

rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 47:     output_dir = getwd(), ...)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()52:         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: 34: doTryCatch(return(expr), name, parentenv, handler)
    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()doWithOneRestart(return(expr), restart)55: 
tryCatchOne(expr, names, parentenv, handlers[[1L]])35:         if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])

            error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {36: 56: tryCatchList(expr, classes, parentenv, handlers)
57:     setwd(wd)tryCatch({    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(), ...)
    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6ekfKA/file6b5171c3984a.rds")
An irrecoverable exception occurred. R is aborting now ...
54: doTryCatch(return(expr), name, parentenv, handler)
        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({    engine$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)}, 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)         output <- find_vignette_product(name, by = "texi2pdf",             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$include)             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58:             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6ekfKA/file6b5171c3984a.rds")42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: 
An irrecoverable exception occurred. R is aborting now ...
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/Rtmp6ekfKA/file6b5171c3984a.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