Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-10 14:45:01.329 R[43340:63093] 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, ...)

Traceback:
 8:  1: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
RowCumsum(valid)
 2: 11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     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]]    validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())
 3:     }    invisible(structure(msg, class = "try-error", condition = e))})SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius, 
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$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, ...)17: 
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 
Traceback:

Traceback:
tryCatch(expr, error = function(e) { 1: RowCumsum(valid)
doTryCatch(return(expr), name, parentenv, handler)    call <- conditionCall(e) 2:     if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch))) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 
 1:             call <- sys.call(-4L)    validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 18: RowCumsum(valid)tryCatchOne(expr, names, parentenv, handlers[[1L]])        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) 

    verbose = verbose) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 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)            prefix <- paste0(prefix, "\n  ")
    }22:  3: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     else prefix <- "Error : "    E = E, showPlot = TRUE)    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,         cat(msg, file = outFile)    tau = tau, theta = th, exclusionRadius = exclusionRadius,         .Internal(printDeferredWarnings())    validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     }    embedded = embedded, validLib = validLib, noTime = noTime,     verbose = verbose)    invisible(structure(msg, class = "try-error", condition = e))24: 
})
    ignoreNan = ignoreNan, backend = backend) 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, eval(expr, envir)

25: eval(expr, envir)
26:  4: withVisible(eval(expr, envir))12: 
27: withCallingHandlers(code, error = function (e)     ignoreNan = ignoreNan, backend = backend)ComputeError(predictions$Observations, predictions$Predictions)
rlang::entrace(e), message = function (cnd) try(lapply(X = S, FUN = FUN, ...), silent = TRUE)

13:  5: {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 4: 
14: FUN(X[[i]], ...)    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 
    embedded = embedded, validLib = validLib, noTime = noTime, ComputeError(predictions$Observations, predictions$Predictions)    watcher$capture_plot_and_output()
15:     ignoreNan = ignoreNan, backend = backend)$predictions) 5: lapply(seq_len(cores), inner.do)    if (on_message$capture) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,         watcher$push(cnd)
 6: 
    }    if (on_message$silence) {16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)        invokeRestart("muffleMessage")
FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)    embedded = embedded, validLib = validLib, noTime = noTime, 
    } 9:     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: 18: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])


}, warning = function (cnd) 10: { 7:     if (getOption("warn") >= 2 || getOption("warn") < 0) {tryCatchList(expr, classes, parentenv, handlers)lapply(X = S, FUN = FUN, ...)        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)
        watcher$push(cnd)19: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    }    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch))) 20:     if (on_warning$silence) {            call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 
        invokeRestart("muffleWarning") 8: doTryCatch(return(expr), name, parentenv, handler)    mc.preschedule = TRUE), error = function(e) NULL)
 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)) {
        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")    }        if (is.na(w))         if (identical(call[[1L]], quote(doTryCatch)))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],             call <- sys.call(-4L)21:                 type = "b")}, error = function (cnd)         if (w > LONG) {SweepApply(theta, worker, numProcess)
        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)        sm <- strsplit(conditionMessage(e), "\n")[[1L]]22:     watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
28:         w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],             prefix <- paste0(prefix, "\n  ")eval(call)
29:     }unlist(SweepApply(theta, worker, numProcess))    else prefix <- "Error : "
                type = "b")    msg <- paste0(prefix, conditionMessage(e), "\n")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {23:     }        cat(msg, file = outFile)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", eval(call)
30: with_handlers({    for (expr in tle$exprs) {    target = "Thrips_imaginis", lib = "1 73", pred = "1 73",         .Internal(printDeferredWarnings())        ev <- withVisible(eval(expr, envir))    E = E, showPlot = TRUE)
    }24:     else prefix <- "Error : "    invisible(structure(msg, class = "try-error", condition = e))    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))eval(expr, envir)        watcher$capture_plot_and_output()    if (!silent && isTRUE(getOption("show.error.messages"))) {})
25:         cat(msg, file = outFile)        watcher$print_value(ev$value, ev$visible, envir)        .Internal(printDeferredWarnings())    }
12: eval(expr, envir)
    }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)    invisible(structure(msg, class = "try-error", condition = e))    TRUE}, handlers)
26: })withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE){    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }
31: 
doWithOneRestart(return(expr), restart)    if (on_message$silence) {        invokeRestart("muffleMessage")    }13: 
}, warning = function (cnd) 32: withOneRestart(expr, restarts[[1L]])
{33: withRestartList(expr, restarts[-nr])
    if (getOption("warn") >= 2 || getOption("warn") < 0) {
14: 34:         return()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)doWithOneRestart(return(expr), restart)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: 
tryCatchOne(expr, names, parentenv, handlers[[1L]])    }35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
FUN(X[[i]], ...)
36: 
withRestartList(expr, restarts)    watcher$capture_plot_and_output()19: tryCatchList(expr, classes, parentenv, handlers)    if (on_warning$capture) {
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,         cnd <- sanitize_call(cnd)
        watcher$push(cnd)37: withRestarts(with_handlers({    for (expr in tle$exprs) {    mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
    }22: unlist(SweepApply(theta, worker, numProcess))    if (on_warning$silence) {
23:         invokeRestart("muffleWarning")    }        ev <- withVisible(eval(expr, envir))}, error = function (cnd) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)15:     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: eval(expr, envir)    }    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})

28: eval(call)
29: 25: eval(call)lapply(seq_len(cores), inner.do)
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)eval(expr, envir)    TRUE    }

    TRUE26: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, handlers)16: 
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
31: 
18: doWithOneRestart(return(expr), restart)withVisible(eval(expr, envir))
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])

35: 19: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatchList(expr, classes, parentenv, handlers)

20: 27: 38: 
withCallingHandlers(code, error = function (e) evaluate::evaluate(...)rlang::entrace(e), message = function (cnd) {36: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 
    mc.preschedule = TRUE), error = function(e) NULL)    watcher$capture_plot_and_output()withRestartList(expr, restarts)
37: 39: 
21: SweepApply(theta, worker, numProcess)
    if (on_message$capture) {22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, unlist(SweepApply(theta, worker, numProcess))withRestarts(with_handlers({        watcher$push(cnd)
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    for (expr in tle$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)    keep_message = if (is.numeric(options$message)) TRUE else options$message,     watcher$capture_plot_and_output()    if (on_message$capture) {    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
        watcher$push(cnd)
    }    if (on_message$silence) {    }    if (on_message$silence) {38: 41: 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$render, options))
40: in_dir(input_dir(), expr)        invokeRestart("muffleMessage")in_input_dir(evaluate(code, envir = env, new_device = FALSE,     }    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, warning = function (cnd)         invokeRestart("muffleMessage")    keep_message = if (is.numeric(options$message)) TRUE else options$message, {
    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }    stop_on_error = if (is.numeric(options$error)) options$error else {}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    }    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})}, warning = function (cnd) 
        if (options$error && options$include)             0L{            0L    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()        else 2L    }, output_handler = knit_handlers(options$render, options)))        else 2L    }, output_handler = knit_handlers(options$render, options)))
42:     if (on_warning$capture) {
        cnd <- sanitize_call(cnd)42: 28: eng_r(options)eval(call)
eng_r(options)
43:         watcher$push(cnd)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), block_exec(params)    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)
29: 44:     }    }), list(rlang_trace_top_env = knit_global())), function(loc) {    if (on_warning$silence) {    setwd(wd)eval(call)call_block(x)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        invokeRestart("muffleWarning")
    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)    }}, error = function (cnd) 45:         watcher$capture_plot_and_output()
        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
{
process_group(group)
46: 31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {    watcher$capture_plot_and_output()        if (progress && is.function(pb$interrupt)) 51:     cnd <- sanitize_call(cnd)            pb$interrupt()doWithOneRestart(return(expr), restart)
32:     watcher$push(cnd)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),         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)    output_dir = getwd(), ...)withOneRestart(expr, restarts[[1L]])
    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})    write_utf8(res, output %n% stdout())

    paste0("\nQuitting from ", loc, if (!is.null(error)) 28: 33: withRestartList(expr, restarts[-nr])
52: eval(call)34: doWithOneRestart(return(expr), restart)

35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
        paste0("\n", rule(), error, "\n", rule()))36: withRestartList(expr, restarts)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)29: 

49: process_file(text, output)vweave_rmarkdown(...)
eval(call)37: 53: 
withRestarts(with_handlers({engine$weave(file, quiet = quiet, encoding = enc)30:     for (expr in tle$exprs) {
        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()54: 
        watcher$print_value(ev$value, ev$visible, envir)doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {    }        texi2pdf(file = output, clean = FALSE, quiet = quiet)        watcher$print_value(ev$value, ev$visible, envir)        output <- find_vignette_product(name, by = "texi2pdf",     }    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 2L50:     }, output_handler = knit_handlers(options$render, options))            engine = engine)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)    TRUE}, handlers)
40: 
in_dir(input_dir(), expr)51:     }rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    outputs <- c(outputs, output)52: 31: doWithOneRestart(return(expr), restart)
    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, error = function(e) {vweave_rmarkdown(...)    thisOK <<- FALSE    keep_message = if (is.numeric(options$message)) TRUE else options$message,     fails <<- c(fails, file)
53: engine$weave(file, quiet = quiet, encoding = enc)    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: 54: eng_r(options)
43:     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", doTryCatch(return(expr), name, parentenv, handler)block_exec(params)32: 
44:         file, conditionMessage(e)))
withOneRestart(expr, restarts[[1L]])55: 
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])call_block(x)

})
56: 
58: tryCatchList(expr, classes, parentenv, handlers)45: 
35: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpnyv6kC/file6bab74b233e5.rds")
An irrecoverable exception occurred. R is aborting now ...
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: process_group(group)57: 
tryCatch({withRestartList(expr, restarts)    engine$weave(file, quiet = quiet, encoding = enc)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))    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) {46:     thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)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/Rtmpnyv6kC/file6bab74b233e5.rds")
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)    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,     })
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)    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$render, options))
    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43:     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(), ...)block_exec(params)
44: call_block(x)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)

45: process_group(group)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)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)    })
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpnyv6kC/file6bab74b233e5.rds")
An irrecoverable exception occurred. R is aborting now ...
    error = function(e) {        if (progress && is.function(pb$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/Rtmpnyv6kC/file6bab74b233e5.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