Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-12 13:46:08.827 R[41558:60426] XType: Using static font registry.

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

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

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

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

Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$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: 
Traceback:
 1: RowCumsum(valid)
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),  2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())  3:             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
Traceback:

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)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 
 1: RowCumsum(valid)51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     tau = tau, theta = th, exclusionRadius = exclusionRadius, 
    output_dir = getwd(), ...)
52:     embedded = embedded, validLib = validLib, noTime = noTime, vweave_rmarkdown(...)    ignoreNan = ignoreNan, backend = backend)
 4: ComputeError(predictions$Observations, predictions$Predictions)
 5:  2: 
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
53:  3: engine$weave(file, quiet = quiet, encoding = enc)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)
    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 
54:     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
doTryCatch(return(expr), name, parentenv, handler)
55:  6: FUN(X[[i]], ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: 10: tryCatchList(expr, classes, parentenv, handlers)
56: tryCatchList(expr, classes, parentenv, handlers)
11: 57: tryCatch(expr, error = function(e) {tryCatch({    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch))) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     engine$weave(file, quiet = quiet, encoding = enc)    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     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)    }    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)            call <- sys.call(-4L)
 6: FUN(X[[i]], ...)
    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e))) 7: lapply(X = S, FUN = FUN, ...)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")
10: })
Traceback:
        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)        if (is.na(w)) 
tryCatchList(expr, classes, parentenv, handlers)
 3:             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")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/Rtmp0e268T/file6b93745ca51f.rds")
An irrecoverable exception occurred. R is aborting now ...
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,     tau = tau, theta = th, exclusionRadius = exclusionRadius,         if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)
    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))})
 4: ComputeError(predictions$Observations, predictions$Predictions)
 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 11: tryCatch(expr, error = function(e) {12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))    knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     call <- conditionCall(e)    if (!is.null(call)) {    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
 7: 
14: FUN(X[[i]], ...)
        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)lapply(X = S, FUN = FUN, ...)
 8:         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) doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])            prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "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)
10:     msg <- paste0(prefix, conditionMessage(e), "\n")tryCatchList(expr, classes, parentenv, handlers)    .Internal(seterrmessage(msg[1L]))
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 
11: tryCatchList(expr, classes, parentenv, handlers)
tryCatch(expr, error = function(e) {20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)
    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    call <- conditionCall(e)    if (!is.null(call)) {21:         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))     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)            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
17: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))

23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",                 type = "b")18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     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)         if (w > LONG) rlang::entrace(e), message = function (cnd)             prefix <- paste0(prefix, "\n  "){    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    mc.preschedule = TRUE), error = function(e) NULL)    }    .Internal(seterrmessage(msg[1L]))    if (on_message$silence) {        invokeRestart("muffleMessage")    }
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: }, warning = function (cnd) {    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)    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")
    }24: eval(expr, envir)
    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))}, error = function (cnd) {25: eval(expr, envir)
    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)})

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)28: eval(call)

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)29: eval(call)26: withVisible(eval(expr, envir))

30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: 27: withRestartList(expr, restarts[-nr])withCallingHandlers(code, error = function (e) 
rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)
22:     }    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$capture) {34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", withRestartList(expr, restarts)
37:     target = "Thrips_imaginis", lib = "1 73", pred = "1 73",     E = E, showPlot = TRUE)        cnd <- sanitize_call(cnd)        watcher$push(cnd)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }    }    if (on_warning$silence) {        invokeRestart("muffleWarning")withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }}, error = function (cnd) {    watcher$capture_plot_and_output()}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    cnd <- sanitize_call(cnd)    watcher$push(cnd)    }    watcher$capture_plot_and_output()    TRUE    switch(on_error, continue = invokeRestart("eval_continue"),     if (on_warning$capture) {}, 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,         cnd <- sanitize_call(cnd)    keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)        stop = invokeRestart("eval_stop"), error = NULL)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})        if (options$error && options$include) })
28: eval(call)            0L
29: eval(call)
        else 2L    }, output_handler = knit_handlers(options$render, options))

28: 40: 30: eval(call)with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))
29: eval(call)
        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
in_dir(input_dir(), expr)
31: 30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)doWithOneRestart(return(expr), restart)
41: 
32: 31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])in_input_dir(evaluate(code, envir = env, new_device = FALSE, 

33: withRestartList(expr, restarts[-nr])
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 34: doWithOneRestart(return(expr), restart)36:     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) 
withRestartList(expr, restarts)            0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])

42: 36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()37: eng_r(options)
withRestarts(with_handlers({    for (expr in tle$exprs) {43: block_exec(params)
44: call_block(x)
45:         watcher$print_value(ev$value, ev$visible, envir)        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    }    TRUEprocess_group(group)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
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()) 38:     TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38:             error <<- format(e)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 {evaluate::evaluate(...)
39:         if (options$error && options$include) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     })
47:     keep_message = if (is.numeric(options$message)) TRUE else options$message, with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()            0L        else 2L        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     }), list(rlang_trace_top_env = knit_global()))

    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     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) 48:     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
            0L        else 2L42: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     }, output_handler = knit_handlers(options$render, options)))eng_r(options)
43: block_exec(params)
44: call_block(x)
42: eng_r(options)
43: block_exec(params)
44: call_block(x)

45: process_group(group)    error = function(e) {        if (progress && is.function(pb$interrupt)) 
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())         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()))
            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 (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)48: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)    })

49: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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(), ...)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {52: vweave_rmarkdown(...)        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
    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)53: 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)        paste0("\n", rule(), error, "\n", rule()))    }), list(rlang_trace_top_env = knit_global())), function(loc) {engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
        paste0("\n", rule(), error, "\n", rule()))49: process_file(text, output)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
55: 
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])50: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)doTryCatch(return(expr), name, parentenv, handler)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)56: tryCatchList(expr, classes, parentenv, handlers)
55: 
57: tryCatch({tryCatchOne(expr, names, parentenv, handlers[[1L]])    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)56: tryCatchList(expr, classes, parentenv, handlers)    output <- find_vignette_product(name, by = "weave", engine = engine)
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf", 52:             engine = engine)    }    outputs <- c(outputs, output)    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)}, error = function(e) {    thisOK <<- FALSE    }    outputs <- c(outputs, output)}, error = function(e) {vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)    thisOK <<- FALSE
54: doTryCatch(return(expr), name, parentenv, handler)
    fails <<- c(fails, file)55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp0e268T/file6b93745ca51f.rds")
An irrecoverable exception occurred. R is aborting now ...
57:     fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
tryCatch({58:     engine$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)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp0e268T/file6b93745ca51f.rds")
An irrecoverable exception occurred. R is aborting now ...
        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/Rtmp0e268T/file6b93745ca51f.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