Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-08 16:22:33.295 R[40839:59518] 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)

Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,  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]], ...)
    validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose) 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)
 3: 
 9: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])
10:     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))  8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)            call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L
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],         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)                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")            prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
12: 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: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)
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: 
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])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))
Traceback:
 1: RowCumsum(valid)19: 
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: 
 2: tryCatchList(expr, classes, parentenv, handlers)
20: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 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)    mc.preschedule = TRUE), error = function(e) NULL)
21: eval(expr, envir)
Traceback:

 1: 25: RowCumsum(valid)SweepApply(theta, worker, numProcess)
22: 

 2:  4: eval(expr, envir)
unlist(SweepApply(theta, worker, numProcess))FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 26: withVisible(eval(expr, envir))
27:     validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 
    verbose = verbose)23: ComputeError(predictions$Observations, predictions$Predictions)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 
withCallingHandlers(code, error = function (e)     target = "Thrips_imaginis", lib = "1 73", pred = "1 73", rlang::entrace(e), message = function (cnd) 
{ 3:     E = E, showPlot = TRUE) 5: 
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     watcher$capture_plot_and_output()SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     if (on_message$capture) {    tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,  5:     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)        watcher$push(cnd)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     }    if (on_message$silence) {        invokeRestart("muffleMessage")    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     }{    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {    embedded = embedded, validLib = validLib, noTime = noTime, 
}, warning = function (cnd)     ignoreNan = ignoreNan, backend = backend)$predictions) 6: FUN(X[[i]], ...){        invokeRestart("muffleMessage")    }    if (getOption("warn") >= 2 || getOption("warn") < 0) {}, warning = function (cnd) {

    if (getOption("warn") >= 2 || getOption("warn") < 0) { 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 7:         return()        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)lapply(X = S, FUN = FUN, ...)        watcher$push(cnd)    }    }    if (on_warning$silence) { 8:     watcher$capture_plot_and_output()        invokeRestart("muffleWarning")    if (on_warning$capture) {
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])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")        cnd <- sanitize_call(cnd)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    }        watcher$push(cnd)        if (is.na(w)) }, error = function (cnd) {        sm <- strsplit(conditionMessage(e), "\n")[[1L]]    }        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))     if (on_warning$silence) {        invokeRestart("muffleWarning")            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],     watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],     watcher$push(cnd)                type = "b")    }}, error = function (cnd)                 type = "b")    switch(on_error, continue = invokeRestart("eval_continue"),         if (w > LONG)         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"))) {        stop = invokeRestart("eval_stop"), error = NULL)        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }            prefix <- paste0(prefix, "\n  ")    invisible(structure(msg, class = "try-error", condition = e)){})
})    }
28: eval(call)
    else prefix <- "Error : "29: eval(call)    msg <- paste0(prefix, conditionMessage(e), "\n")12:     .Internal(seterrmessage(msg[1L]))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
30: with_handlers({
    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)13:     watcher$capture_plot_and_output()    if (!silent && isTRUE(getOption("show.error.messages"))) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))    cnd <- sanitize_call(cnd)
14: FUN(X[[i]], ...)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})    }        cat(msg, file = outFile)
28: eval(call)        .Internal(printDeferredWarnings())
    }    invisible(structure(msg, class = "try-error", condition = e))    TRUE}, handlers)

15: 29: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: eval(call)doTryCatch(return(expr), name, parentenv, handler)
})31: 
18: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)


13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))30: 32: withOneRestart(expr, restarts[[1L]])with_handlers({19: 
tryCatchList(expr, classes, parentenv, handlers)33:     for (expr in tle$exprs) {withRestartList(expr, restarts[-nr])
14: 
FUN(X[[i]], ...)
20:         ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)
34: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     }    TRUE15: doWithOneRestart(return(expr), restart)
35: }, handlers)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])lapply(seq_len(cores), inner.do)
36: withRestartList(expr, restarts)


37: withRestarts(with_handlers({    for (expr in tle$exprs) {    mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: 16:         ev <- withVisible(eval(expr, envir))31: unlist(SweepApply(theta, worker, numProcess))
doWithOneRestart(return(expr), restart)
32:         watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73", withOneRestart(expr, restarts[[1L]])parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18:     E = E, showPlot = TRUE)
33: withRestartList(expr, restarts[-nr])
tryCatchOne(expr, names, parentenv, handlers[[1L]])34: 
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)

24: eval(expr, envir)
25: eval(expr, envir)38: 
26: withVisible(eval(expr, envir))
doWithOneRestart(return(expr), restart)
35: evaluate::evaluate(...)27: 
39: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    if (on_message$capture) {    for (expr in tle$exprs) {19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,         ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()    keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchList(expr, classes, parentenv, handlers)    stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        watcher$print_value(ev$value, ev$visible, envir)        else 2L    }, output_handler = knit_handlers(options$render, options))
40:         watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }    }in_dir(input_dir(), expr)
    TRUE
}, warning = function (cnd) 41: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
{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, 20:     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0LtryCatch(parallel::mclapply(values, worker, mc.cores = cores,         else 2L    if (getOption("warn") >= 2 || getOption("warn") < 0) {38: evaluate::evaluate(...)
39:     }, output_handler = knit_handlers(options$render, options)))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {            0L        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())     mc.preschedule = TRUE), error = function(e) NULL)
        else 2L21:             error <<- format(e)    })
    }, output_handler = knit_handlers(options$render, options))        return()47: 
    }    watcher$capture_plot_and_output()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     if (on_warning$capture) {        cnd <- sanitize_call(cnd)    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())         watcher$push(cnd)            error <<- format(e)    }    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), SweepApply(theta, worker, numProcess)    error = function(e) {        if (progress && is.function(pb$interrupt))     if (on_warning$silence) {            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)        invokeRestart("muffleWarning")40:     }}, 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$visible, envir)    }    TRUE    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
}, handlers)in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))


52: vweave_rmarkdown(...)31: 22: 42: 
unlist(SweepApply(theta, worker, numProcess))eng_r(options)
23: doWithOneRestart(return(expr), restart)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: 53: 

eval(expr, envir)
32: 43: withOneRestart(expr, restarts[[1L]])25: engine$weave(file, quiet = quiet, encoding = enc)eval(expr, envir)
33: 
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()withRestartList(expr, restarts[-nr])
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }        if (is_R_CMD_build() || is_R_CMD_check()) 
34: 
    if (on_message$silence) {        invokeRestart("muffleMessage")doWithOneRestart(return(expr), restart)    }}, warning = function (cnd) {56:             error <<- format(e)    })    if (getOption("warn") >= 2 || getOption("warn") < 0) {
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
        return()
47: 36: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check()) withRestartList(expr, restarts)            error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
tryCatchList(expr, classes, parentenv, handlers)37: 

57: 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))    error = function(e) {        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    setwd(startdir)        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    output <- find_vignette_product(name, by = "weave", engine = engine)    }    TRUE    }), list(rlang_trace_top_env = knit_global())), function(loc) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)    setwd(wd)
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)     if (!have.makefile && vignette_is_tex(output)) {            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$include)             0L        else 2L    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)        texi2pdf(file = output, clean = FALSE, quiet = quiet)    watcher$capture_plot_and_output()
        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 (on_warning$capture) {    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: 58: 49: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",         cnd <- sanitize_call(cnd)block_exec(params)        watcher$push(cnd)process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2a3B99/file6b1814d54475.rds")
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)    }
55: 
tryCatchOne(expr, names, parentenv, handlers[[1L]])    })
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())     if (on_warning$silence) {            error <<- format(e)
An irrecoverable exception occurred. R is aborting now ...
        invokeRestart("muffleWarning")    }}, error = function (cnd) {56:     watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
tryCatchList(expr, classes, parentenv, handlers)
28: eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))    error = function(e) {57:         if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    }), list(rlang_trace_top_env = knit_global())), function(loc) {        watcher$capture_plot_and_output()    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58:         watcher$print_value(ev$value, ev$visible, envir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     }    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))    TRUE}, 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:     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2a3B99/file6b1814d54475.rds")}, handlers)vweave_rmarkdown(...)
53: 

An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: 56: tryCatchList(expr, classes, parentenv, handlers)
doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
57: tryCatch({    engine$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)33: }, error = function(e) {withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])    thisOK <<- FALSE
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)    }    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58:     TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2a3B99/file6b1814d54475.rds")

38: An irrecoverable exception occurred. R is aborting now ...
evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2a3B99/file6b1814d54475.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