Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-15 17:35:27.796 R[40711:59329] 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:

Traceback:
 1: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)

Traceback:
 1:  1: RowCumsum(valid)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,  2: RowCumsum(valid)
 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
 3: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,     validLib = validLib, libOverlap = idx$libOverlap, backend = backend,     verbose = verbose)
    tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime, 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)    ignoreNan = ignoreNan, backend = backend)
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,  4:     tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)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)$predictions)
 6: FUN(X[[i]], ...)
 7: lapply(X = S, FUN = FUN, ...)
 8:  4: ComputeError(predictions$Observations, predictions$Predictions)
 5:  4: ComputeError(predictions$Observations, predictions$Predictions)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,  5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,     embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)

 7: lapply(X = S, FUN = FUN, ...) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])

 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 10: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {    ignoreNan = ignoreNan, backend = backend)$predictions)
 6: FUN(X[[i]], ...)
11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)
 7: lapply(X = S, FUN = FUN, ...)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch))) 
 8:             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[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 <- 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 : "
10: tryCatchList(expr, classes, parentenv, handlers)            prefix <- paste0(prefix, "\n  ")
    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))11: tryCatch(expr, error = function(e) {    if (!silent && isTRUE(getOption("show.error.messages"))) {    call <- conditionCall(e)    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))         cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    if (!silent && isTRUE(getOption("show.error.messages"))) {    invisible(structure(msg, class = "try-error", condition = e))        cat(msg, file = outFile)})
12:             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))         .Internal(printDeferredWarnings())            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],     }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
    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]], ...)

13: 15: lapply(seq_len(cores), inner.do)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
                type = "b")16: 14: FUN(X[[i]], ...)
15: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])        if (w > LONG) 
lapply(seq_len(cores), inner.do)
16:             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     .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))})
    mc.preschedule = TRUE), error = function(e) NULL)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
Traceback:

17: doTryCatch(return(expr), name, parentenv, handler) 1: 
RowCumsum(valid)

 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 21: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])    validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 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: 

13: eval(expr, envir)19:     verbose = verbose)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
25: 
 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 
tryCatchList(expr, classes, parentenv, handlers)14: FUN(X[[i]], ...)
20:     tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     mc.preschedule = TRUE), error = function(e) NULL)

21: SweepApply(theta, worker, numProcess)    embedded = embedded, validLib = validLib, noTime = noTime,     ignoreNan = ignoreNan, backend = backend)eval(expr, envir)
15: 

22:  4: unlist(SweepApply(theta, worker, numProcess))ComputeError(predictions$Observations, predictions$Predictions)26: 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: 
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")    }
tryCatchList(expr, classes, parentenv, handlers)
23: }, warning = function (cnd) {20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",  5:     if (getOption("warn") >= 2 || getOption("warn") < 0) {    target = "Thrips_imaginis", lib = "1 73", pred = "1 73",         return()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)    E = E, showPlot = TRUE)

24: eval(expr, envir) 6: 
FUN(X[[i]], ...)
    }    watcher$capture_plot_and_output()    mc.preschedule = TRUE), error = function(e) NULL) 7:     if (on_warning$capture) {25: lapply(X = S, FUN = FUN, ...)
        cnd <- sanitize_call(cnd)21: SweepApply(theta, worker, numProcess)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }
eval(expr, envir) 8: 
doTryCatch(return(expr), name, parentenv, handler)
}, error = function (cnd) 
22: unlist(SweepApply(theta, worker, numProcess))
 9: 26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",     target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 
    E = E, showPlot = TRUE)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)rlang::entrace(e), message = function (cnd)         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], 24:                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n"){eval(expr, envir)
25:     watcher$capture_plot_and_output()    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         .Internal(printDeferredWarnings())    }        stop = invokeRestart("eval_stop"), error = NULL)    watcher$capture_plot_and_output()    if (on_message$capture) {    invisible(structure(msg, class = "try-error", condition = e))})})
12: eval(expr, envir)

28: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)eval(call)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
        watcher$push(cnd)    }
    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {14: 26: FUN(X[[i]], ...)29: eval(call)
30: with_handlers({
    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        return()        watcher$capture_plot_and_output()    }    watcher$capture_plot_and_output()15:     if (on_warning$capture) {        cnd <- sanitize_call(cnd)withVisible(eval(expr, envir))        watcher$push(cnd)lapply(seq_len(cores), inner.do)

16: 27:     }        watcher$print_value(ev$value, ev$visible, envir)    if (on_warning$silence) {withCallingHandlers(code, error = function (e)     }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)rlang::entrace(e), message = function (cnd)         invokeRestart("muffleWarning")
    TRUE}, handlers){
31:     }}, error = function (cnd) doWithOneRestart(return(expr), restart)    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)17:     }doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    if (on_message$silence) {
32: {    watcher$capture_plot_and_output()19:         invokeRestart("muffleMessage")tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,     }    cnd <- sanitize_call(cnd)    watcher$push(cnd)withOneRestart(expr, restarts[[1L]])    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", 33:     E = E, showPlot = TRUE)    switch(on_error, continue = invokeRestart("eval_continue"), withRestartList(expr, restarts[-nr])}, warning = function (cnd) 
34: {    if (getOption("warn") >= 2 || getOption("warn") < 0) {
        return()        stop = invokeRestart("eval_stop"), error = NULL)})    }    watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart)
28: 24: 
eval(call)
29: eval(call)
30: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()    if (on_warning$capture) {35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
        watcher$print_value(ev$value, ev$visible, envir)        cnd <- sanitize_call(cnd)eval(expr, envir)        watcher$push(cnd)37: withRestarts(with_handlers({    }
    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    TRUE25: }, handlers)eval(expr, envir)
26:     watcher$capture_plot_and_output()withVisible(eval(expr, envir))    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),     for (expr in tle$exprs) {
31: 
doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])        ev <- withVisible(eval(expr, envir))27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {
34: doWithOneRestart(return(expr), restart)
        stop = invokeRestart("eval_stop"), error = NULL)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37:     watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }})    TRUE}, warning = function (cnd) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
withRestarts(with_handlers({    if (getOption("warn") >= 2 || getOption("warn") < 0) {    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))38:         return()evaluate::evaluate(...)
    }    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
        watcher$capture_plot_and_output()
28: 39:         watcher$print_value(ev$value, ev$visible, envir)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)eval(call)
28: 29: eval(call)
    stop_on_error = if (is.numeric(options$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: evaluate::evaluate(...)
39: eval(call)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 
30:     keep_message = if (is.numeric(options$message)) TRUE else options$message, 41: 29: 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, with_handlers({    stop_on_error = if (is.numeric(options$error)) options$error else {    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)    stop_on_error = if (is.numeric(options$error)) options$error else {
eval(call)
31:         if (options$error && options$include) 30:             0L        else 2Lwith_handlers({        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: doWithOneRestart(return(expr), restart)
    for (expr in tle$exprs) {32: eng_r(options)withOneRestart(expr, restarts[[1L]])    }, output_handler = knit_handlers(options$render, options))

33: withRestartList(expr, restarts[-nr])        ev <- withVisible(eval(expr, envir))40:         watcher$capture_plot_and_output()in_dir(input_dir(), expr)
34: doWithOneRestart(return(expr), restart)        watcher$print_value(ev$value, ev$visible, envir)
43:     }    TRUE
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, 
}, handlers)35: block_exec(params)
31: doWithOneRestart(return(expr), restart)

32: withOneRestart(expr, restarts[[1L]])
33:     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include) 44:             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))withRestartList(expr, restarts[-nr])

34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
42: 36: withRestartList(expr, restarts)eng_r(options)call_block(x)
43: block_exec(params)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])

36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))37:         watcher$capture_plot_and_output()withRestarts(with_handlers({        watcher$print_value(ev$value, ev$visible, envir)    for (expr in tle$exprs) {    }    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))

45: process_group(group)40:         ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }44: call_block(x)
45: process_group(group)
46: 
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     TRUE    error = function(e) {in_dir(input_dir(), expr)46: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
38:         if (progress && is.function(pb$interrupt)) evaluate::evaluate(...)
39:             pb$interrupt()
        if (is_R_CMD_build() || is_R_CMD_check()) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,             error <<- format(e)    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), 41:     keep_message = if (is.numeric(options$message)) TRUE else options$message, in_input_dir(evaluate(code, envir = env, new_device = FALSE,     error = function(e) {    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 {    error = function(e) {        if (progress && is.function(pb$interrupt))         if (options$error && options$include)             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             0L            error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))        else 2L
    stop_on_error = if (is.numeric(options$error)) options$error else {    }, output_handler = knit_handlers(options$render, options))
48:         if (options$error && options$include)             0L40:         if (progress && is.function(pb$interrupt)) in_dir(input_dir(), expr)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,             pb$interrupt()    error = function(e) {        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    keep_message = if (is.numeric(options$message)) TRUE else options$message,         if (progress && is.function(pb$interrupt))     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))    setwd(wd)            pb$interrupt()    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         if (is_R_CMD_build() || is_R_CMD_check())         paste0("\n", rule(), error, "\n", rule()))        else 2L
            error <<- format(e)    }, output_handler = knit_handlers(options$render, options)))
    }), list(rlang_trace_top_env = knit_global())), function(loc) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)    setwd(wd)    write_utf8(res, output %n% stdout())
42: 49:     paste0("\nQuitting from ", loc, if (!is.null(error)) eng_r(options)        paste0("\n", rule(), error, "\n", rule()))42: 
eng_r(options)
43: block_exec(params)
43: 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(), ...)
52: vweave_rmarkdown(...)block_exec(params)

53: 44: 
call_block(x)engine$weave(file, quiet = quiet, encoding = enc)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)

45: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 44: process_group(group)
call_block(x)

45:     output_dir = getwd(), ...)46: process_group(group)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46:             pb$interrupt()withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 56: tryCatchList(expr, classes, parentenv, handlers)        if (is_R_CMD_build() || is_R_CMD_check()) 54:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })

doTryCatch(return(expr), name, parentenv, handler)            error <<- format(e)57:     })

tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)47: 47: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    output <- find_vignette_product(name, by = "weave", engine = engine)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     setwd(startdir)        output <- find_vignette_product(name, by = "texi2pdf",     error = function(e) {        if (progress && is.function(pb$interrupt))     error = function(e) {            pb$interrupt()        if (progress && is.function(pb$interrupt))         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))            engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))
            pb$interrupt()48:     output <- find_vignette_product(name, by = "weave", engine = engine)})xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),         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 (!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) {    }
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/RtmpMCNwOz/file6b1a64f3853f.rds")
An irrecoverable exception occurred. R is aborting now ...
    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/RtmpMCNwOz/file6b1a64f3853f.rds")
An irrecoverable exception occurred. R is aborting now ...
        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(), ...)        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)) 
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)        paste0("\n", rule(), error, "\n", rule()))
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)57: tryCatch({
49: process_file(text, output)    engine$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", 
50:             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
52:     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/RtmpMCNwOz/file6b1a64f3853f.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpMCNwOz/file6b1a64f3853f.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