Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-18 15:00:06.291 R[41252:60021] XType: Using static font registry.

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 
Traceback:
    E = E, showPlot = TRUE)
 1: RowCumsum(valid)
 2: 
Traceback:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius, 24: eval(expr, envir)
25:  1: eval(expr, envir)    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)

RowCumsum(valid)
 2: 26: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,  5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, withVisible(eval(expr, envir))    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime, 
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd)     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
{    if (getOption("warn") >= 2 || getOption("warn") < 0) { 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4:         return()ComputeError(predictions$Observations, predictions$Predictions)    }
Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
    watcher$capture_plot_and_output()    tau = tau, theta = th, exclusionRadius = exclusionRadius,     if (on_warning$capture) { 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) { 5:     embedded = embedded, validLib = validLib, noTime = noTime,         invokeRestart("muffleWarning")    }SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, }, error = function (cnd) {    ignoreNan = ignoreNan, backend = backend)
    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     watcher$capture_plot_and_output()
 4: 10:     cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)ComputeError(predictions$Observations, predictions$Predictions)tryCatchList(expr, classes, parentenv, handlers)    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 
    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 30: with_handlers({    embedded = embedded, validLib = validLib, noTime = noTime,     for (expr in tle$exprs) {
11: 
    ignoreNan = ignoreNan, backend = backend)$predictions)        ev <- withVisible(eval(expr, envir))tryCatch(expr, error = function(e) { 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])

10: tryCatchList(expr, classes, parentenv, handlers)
11:  6:         watcher$capture_plot_and_output()FUN(X[[i]], ...)
    call <- conditionCall(e)        watcher$print_value(ev$value, ev$visible, envir)tryCatch(expr, error = function(e) { 7: lapply(X = S, FUN = FUN, ...)
    } 8:     TRUE    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler)            call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L    if (!is.null(call)) {}, handlers)
31:         sm <- strsplit(conditionMessage(e), "\n")[[1L]]doWithOneRestart(return(expr), restart)        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        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],         if (is.na(w))                 type = "b")            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 

32: 10:                 type = "b")tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (w > LONG)         if (identical(call[[1L]], quote(doTryCatch)))             prefix <- paste0(prefix, "\n  ")    }
        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")33:     .Internal(seterrmessage(msg[1L]))    else prefix <- "Error : "withRestartList(expr, restarts[-nr])    if (!silent && isTRUE(getOption("show.error.messages"))) {            call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)    msg <- paste0(prefix, conditionMessage(e), "\n")        prefix <- paste("Error in", dcall, ": ")
        cat(msg, file = outFile)34: doWithOneRestart(return(expr), restart)    .Internal(seterrmessage(msg[1L]))        .Internal(printDeferredWarnings())
35:         LONG <- 75L    }        sm <- strsplit(conditionMessage(e), "\n")[[1L]]withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])    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)
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))     invisible(structure(msg, class = "try-error", condition = e))})            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 13: 
                type = "b")
36: withRestartList(expr, restarts)        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")37: withRestarts(with_handlers({    for (expr in tle$exprs) {12:     }        ev <- withVisible(eval(expr, envir))    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")        watcher$capture_plot_and_output()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
    .Internal(seterrmessage(msg[1L]))        watcher$print_value(ev$value, ev$visible, envir)
16: 13:     if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)    }        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))    TRUEparallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)

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

19: 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: 
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)in_dir(input_dir(), expr)lapply(seq_len(cores), inner.do)

16: tryCatchList(expr, classes, parentenv, handlers)
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)))

20: 42: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)eng_r(options)
43: 22: unlist(SweepApply(theta, worker, numProcess))
block_exec(params)21: SweepApply(theta, worker, numProcess)

23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 

17: 44: call_block(x)doTryCatch(return(expr), name, parentenv, handler)
45: 22: process_group(group)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)    target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 
    E = E, showPlot = TRUE)unlist(SweepApply(theta, worker, numProcess))
20: 46: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {24:     mc.preschedule = TRUE), error = function(e) NULL)        if (progress && is.function(pb$interrupt)) 
21: eval(expr, envir)SweepApply(theta, worker, numProcess)            pb$interrupt()
25: eval(expr, envir)        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) {23:         if (progress && is.function(pb$interrupt)) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)26: 

            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
withVisible(eval(expr, envir))48: 24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))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)27: 

24: eval(expr, envir)withCallingHandlers(code, error = function (e) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
rlang::entrace(e), message = function (cnd)     error = function(e) {{27:     watcher$capture_plot_and_output()25:         if (progress && is.function(pb$interrupt))             pb$interrupt()    if (on_message$capture) {withCallingHandlers(code, error = function (e)         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())eval(expr, envir)        watcher$push(cnd)    paste0("\nQuitting from ", loc, if (!is.null(error)) 
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    }    if (on_message$silence) {        invokeRestart("muffleMessage")    if (on_message$capture) {rlang::entrace(e), message = function (cnd)         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)        watcher$push(cnd)
    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")49:     }process_file(text, output)}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"), {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    }
50:         stop = invokeRestart("eval_stop"), error = NULL)    if (on_message$silence) {        invokeRestart("muffleMessage")    }knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)}, warning = function (cnd) 
{    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }        watcher$push(cnd)51:     watcher$capture_plot_and_output()    if (on_warning$capture) {})
28: eval(call)
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     }    output_dir = getwd(), ...)    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) 29:         cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {{    watcher$capture_plot_and_output()
52:     cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)eval(call)})
30: with_handlers({vweave_rmarkdown(...)    for (expr in tle$exprs) {
28: eval(call)
29: eval(call)
        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()
        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
53: engine$weave(file, quiet = quiet, encoding = enc)    watcher$capture_plot_and_output()
34: 30: doWithOneRestart(return(expr), restart)54:     cnd <- sanitize_call(cnd)
35: with_handlers({    watcher$push(cnd)    for (expr in tle$exprs) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])        ev <- withVisible(eval(expr, envir))    switch(on_error, continue = invokeRestart("eval_continue"),         watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)        stop = invokeRestart("eval_stop"), error = NULL)    if (!have.makefile && vignette_is_tex(output)) {})37: 
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))36: 28:         output <- find_vignette_product(name, by = "texi2pdf",         watcher$capture_plot_and_output()            engine = engine)eval(call)withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE        watcher$capture_plot_and_output()    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))        watcher$print_value(ev$value, ev$visible, envir)})
    }        watcher$print_value(ev$value, ev$visible, envir)58: 
    }    TRUEtools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)29: eval(call)

30: with_handlers({    for (expr in tle$exprs) {    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6gIgHB/file6b5538da2a00.rds")        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }
An irrecoverable exception occurred. R is aborting now ...
    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)    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, 
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$render, options))
40: in_dir(input_dir(), expr)
38:     keep_message = if (is.numeric(options$message)) TRUE else options$message, 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
evaluate::evaluate(...)42: eng_r(options)
43: 
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     stop_on_error = if (is.numeric(options$error)) options$error else {    keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {block_exec(params)        if (options$error && options$include) 
44: call_block(x)
45: process_group(group)
            0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41:         if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
40: in_dir(input_dir(), expr)    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 
46: 41:     keep_message = if (is.numeric(options$message)) TRUE else options$message, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     stop_on_error = if (is.numeric(options$error)) options$error else {    error = function(e) {        if (options$error && options$include)             0Lin_input_dir(evaluate(code, envir = env, new_device = FALSE,         if (progress && is.function(pb$interrupt))     keep_warning = if (is.numeric(options$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$error else {            pb$interrupt()        if (options$error && options$include)         if (is_R_CMD_build() || is_R_CMD_check())             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))            error <<- format(e)    })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$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)) 
42: eng_r(options)
        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
43: 44:             pb$interrupt()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$interrupt)) call_block(x)            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)        if (is_R_CMD_build() || is_R_CMD_check())     }), list(rlang_trace_top_env = knit_global())), function(loc) {
            error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
45: 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)    setwd(wd)process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     write_utf8(res, output %n% stdout())    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
    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)49: process_file(text, output)
50: 49:     }), list(rlang_trace_top_env = knit_global()))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(...)

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)process_file(text, output)
53: 49: engine$weave(file, quiet = quiet, encoding = enc)process_file(text, output)

50: 
54: doTryCatch(return(expr), name, parentenv, handler)
55: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)vweave_rmarkdown(...)

56: 52: vweave_rmarkdown(...)
53: 
engine$weave(file, quiet = quiet, encoding = enc)53: engine$weave(file, quiet = quiet, encoding = enc)
tryCatchList(expr, classes, parentenv, handlers)
57: 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/Rtmp6gIgHB/file6b5538da2a00.rds")

54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({An irrecoverable exception occurred. R is aborting now ...
tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    engine$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",     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)))            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", })
58:         file, conditionMessage(e)))})
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",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6gIgHB/file6b5538da2a00.rds")
An irrecoverable exception occurred. R is aborting now ...
    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6gIgHB/file6b5538da2a00.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