Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-24 15:36:23.665 R[52576:76731] 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)
Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w)) 
 4: ComputeError(predictions$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:             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")FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
    .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)) 8: 
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)doTryCatch(return(expr), name, parentenv, handler)
 9: 
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)

Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))

11: 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: tryCatch(expr, error = function(e) {    call <- conditionCall(e)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    if (!is.null(call)) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) { 3:         invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w)) 
Traceback:
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     if (on_warning$capture) {    tau = tau, theta = th, exclusionRadius = exclusionRadius,  1:         cnd <- sanitize_call(cnd)                type = "b")        watcher$push(cnd)    }        if (w > LONG) RowCumsum(valid)    if (on_warning$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: 
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
            prefix <- paste0(prefix, "\n  ") 3:     }SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     embedded = embedded, validLib = validLib, noTime = noTime, eval(call)
30: with_handlers({    for (expr in tle$exprs) {    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())    tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4:         ev <- withVisible(eval(expr, envir))ComputeError(predictions$Observations, predictions$Predictions)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,         watcher$capture_plot_and_output()    }    ignoreNan = ignoreNan, backend = backend)    invisible(structure(msg, class = "try-error", condition = e))    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)

        watcher$print_value(ev$value, ev$visible, envir)})
12:  4:     }ComputeError(predictions$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)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 7: lapply(X = S, FUN = FUN, ...)    TRUE

13:  6: FUN(X[[i]], ...)}, handlers)

 8:  7: lapply(X = S, FUN = FUN, ...)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))

14: 31: FUN(X[[i]], ...)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)))  8:             call <- sys.call(-4L)
doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10:         dcall <- deparse(call, nlines = 1L)15: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33:         prefix <- paste("Error in", dcall, ": ")withRestartList(expr, restarts[-nr])lapply(seq_len(cores), inner.do)
16: 
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)34: 
17:         LONG <- 75LtryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)        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  ")

18:     }tryCatchOne(expr, names, parentenv, handlers[[1L]])
19:     else prefix <- "Error : "35: 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)    msg <- paste0(prefix, conditionMessage(e), "\n")withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])


    .Internal(seterrmessage(msg[1L]))36:     if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)22: unlist(SweepApply(theta, worker, numProcess))
withRestartList(expr, restarts)23: 
37: 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 <- 75LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",         sm <- strsplit(conditionMessage(e), "\n")[[1L]]withRestarts(with_handlers({    target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)    E = E, showPlot = TRUE)
24: eval(expr, envir)        .Internal(printDeferredWarnings())        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    }    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {39:         cat(msg, file = outFile)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 
    keep_message = if (is.numeric(options$message)) TRUE else options$message,         .Internal(printDeferredWarnings())    invisible(structure(msg, class = "try-error", condition = e))    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))})25:     }
eval(expr, envir)12:     invisible(structure(msg, class = "try-error", condition = e))
26: withVisible(eval(expr, envir))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
})27: 
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))


withCallingHandlers(code, error = function (e) 40: rlang::entrace(e), message = function (cnd) in_dir(input_dir(), expr){    watcher$capture_plot_and_output()14: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)    if (on_message$capture) {FUN(X[[i]], ...)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))

15:         watcher$push(cnd)lapply(seq_len(cores), inner.do)    }
    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {16: 
41: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 14:     if (getOption("warn") >= 2 || getOption("warn") < 0) {    keep_message = if (is.numeric(options$message)) TRUE else options$message,         return()FUN(X[[i]], ...)17:     }    stop_on_error = if (is.numeric(options$error)) options$error else {
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
doTryCatch(return(expr), name, parentenv, handler)
    watcher$capture_plot_and_output()        if (options$error && options$include) 18:     if (on_warning$capture) {        cnd <- sanitize_call(cnd)            0L17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])        watcher$push(cnd)    }    if (on_warning$silence) {        else 2LtryCatchOne(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)
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 
    }, output_handler = knit_handlers(options$render, options)))21:     mc.preschedule = TRUE), error = function(e) NULL)        invokeRestart("muffleWarning")

42:     }}, error = function (cnd) {    watcher$capture_plot_and_output()SweepApply(theta, worker, numProcess)eng_r(options)
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)21: 

SweepApply(theta, worker, numProcess)43:     cnd <- sanitize_call(cnd)
block_exec(params)22: 24:     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]])unlist(SweepApply(theta, worker, numProcess))eval(expr, envir)
23: 
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 33: withRestartList(expr, restarts[-nr])    target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)

34: doWithOneRestart(return(expr), restart)
24: 35: eval(expr, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])

25: eval(expr, envir)

36: 25: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))
26: withVisible(eval(expr, envir))44:         watcher$capture_plot_and_output()eval(expr, envir)call_block(x)
26: withVisible(eval(expr, envir))

27:         watcher$print_value(ev$value, ev$visible, envir)45: withCallingHandlers(code, error = function (e) process_group(group)rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {    }
        watcher$push(cnd)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 
    }    if (on_message$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) {    TRUE            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
27:         invokeRestart("muffleWarning")withCallingHandlers(code, error = function (e) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)rlang::entrace(e), message = function (cnd) 47: {
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {38:         if (progress && is.function(pb$interrupt))     watcher$capture_plot_and_output()evaluate::evaluate(...)
    if (on_message$capture) {    }            pb$interrupt()        watcher$push(cnd)39: }, error = function (cnd) {        if (is_R_CMD_build() || is_R_CMD_check())     watcher$capture_plot_and_output()    }            error <<- format(e)    if (on_message$silence) {        invokeRestart("muffleMessage")evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     }}, warning = function (cnd)     cnd <- sanitize_call(cnd)    watcher$push(cnd){    switch(on_error, continue = invokeRestart("eval_continue"),     }), list(rlang_trace_top_env = knit_global()))        stop = invokeRestart("eval_stop"), error = NULL)    if (getOption("warn") >= 2 || getOption("warn") < 0) {
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     keep_message = if (is.numeric(options$message)) TRUE else options$message,         return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    error = function(e) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)        if (progress && is.function(pb$interrupt))     switch(on_error, continue = invokeRestart("eval_continue"),     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))})            pb$interrupt()
28: eval(call)
        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)
29: eval(call)40:     }), list(rlang_trace_top_env = knit_global())), function(loc) {
    setwd(wd)        stop = invokeRestart("eval_stop"), error = NULL)})
30: 28: eval(call)
29: eval(call)
in_dir(input_dir(), expr)with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31:     write_utf8(res, output %n% stdout())30: with_handlers({    for (expr in tle$exprs) {doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()
    paste0("\nQuitting from ", loc, if (!is.null(error))         watcher$print_value(ev$value, ev$visible, envir)    }    TRUE
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)        paste0("\n", rule(), error, "\n", rule()))}, handlers)41: 
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)

49: process_file(text, output)
50: 35: 31: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
doWithOneRestart(return(expr), restart)36: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withRestartList(expr, restarts)
    keep_message = if (is.numeric(options$message)) TRUE else options$message, 32: 
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$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)withOneRestart(expr, restarts[[1L]])
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 
33: withRestartList(expr, restarts[-nr])    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)

51: 
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     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) 36: 43: block_exec(params)            0L    output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
44: call_block(x)
45: process_group(group)
        else 2L    }, output_handler = knit_handlers(options$render, options))

withRestartList(expr, restarts)40: 
in_dir(input_dir(), expr)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 53: engine$weave(file, quiet = quiet, encoding = enc)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: 
            pb$interrupt()54:         if (is_R_CMD_build() || is_R_CMD_check())     keep_message = if (is.numeric(options$message)) TRUE else options$message,             error <<- format(e)doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)withRestarts(with_handlers({    })    for (expr in tle$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)

57:     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L47:         else 2L38: evaluate::evaluate(...)
tryCatch({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$render, options))
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {    engine$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_handler = knit_handlers(options$render, options)))        if (progress && is.function(pb$interrupt)) in_dir(input_dir(), expr)            pb$interrupt()

41:         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)))})        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), in_input_dir(evaluate(code, envir = env, new_device = FALSE, 42:     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
eng_r(options)        else 2L
43: block_exec(params)58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 
44:     error = function(e) {call_block(x)    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWQIhoU/file84212557b105.rds")    }, output_handler = knit_handlers(options$render, options)))
An irrecoverable exception occurred. R is aborting now ...
        if (progress && is.function(pb$interrupt)) 
            pb$interrupt()42: 
45: process_group(group)
46: eng_r(options)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
        if (is_R_CMD_build() || is_R_CMD_check()) 43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
    error = function(e) {            error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
52: vweave_rmarkdown(...)        if (progress && is.function(pb$interrupt))             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:         if (progress && is.function(pb$interrupt)) 53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)            pb$interrupt()
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
        if (is_R_CMD_build() || is_R_CMD_check()) 56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)            error <<- format(e)    if (!have.makefile && vignette_is_tex(output)) {51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
    })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54:     error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57:         texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatch({        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    engine$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)        if (progress && is.function(pb$interrupt))     }            pb$interrupt()    outputs <- c(outputs, output)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)}, error = function(e) {        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",     }), 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$interrupt))     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)        file, conditionMessage(e)))})    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)
        file, conditionMessage(e)))})49: 58: 
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", process_file(text, output)
    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWQIhoU/file84212557b105.rds")
An irrecoverable exception occurred. R is aborting now ...
    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWQIhoU/file84212557b105.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpWQIhoU/file84212557b105.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