Error(s) in re-building vignettes:
--- re-building ‘clustra_bp_vignette.Rmd’ using rmarkdown

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

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

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)
 2:  2: Predict.matrix(object, dk$data)
 3: Predict.matrix3(object, data)
 4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
 5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size,     newdata.guaranteed, na.action, n.threads, gc.level = gc.level,     ...)
 6: Predict.matrix(object, dk$data)
 3: Predict.matrix3(object, data)mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 8: FUN(X[[i]], ...)
 9: 
 4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
lapply(X = S, FUN = FUN, ...)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
 5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size,     newdata.guaranteed, na.action, n.threads, gc.level = gc.level,     ...)13: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {
 6: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)        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) 
 7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 8: FUN(X[[i]], ...)
 9: lapply(X = S, FUN = FUN, ...)
            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))})
14: 10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: FUN(X[[i]], ...)
17: 13: tryCatch(expr, error = function(e) {lapply(seq_len(cores), inner.do)
    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], 18: parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19: trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose,     ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc,     verbose = TRUE)
                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())    }21: eval(expr, envir)
22: eval(expr, envir)
23: withVisible(eval(expr, envir))
24: 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$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {    invisible(structure(msg, class = "try-error", condition = e))})
14:         return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16:     watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)FUN(X[[i]], ...)
17:     switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})lapply(seq_len(cores), inner.do)
18: 
25: eval(call)parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19: 
26: eval(call)trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose,     ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc,     verbose = TRUE)
27: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE
21: eval(expr, envir)}, handlers)
28: 
22: eval(expr, envir)doWithOneRestart(return(expr), restart)
29: 
23: withVisible(eval(expr, envir))withOneRestart(expr, restarts[[1L]])
30: 
24: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr])
31:     if (on_message$capture) {        watcher$push(cnd)    }doWithOneRestart(return(expr), restart)
32:     if (on_message$silence) {        invokeRestart("muffleMessage")    }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: }, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()withRestartList(expr, restarts)
34:     if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)35: evaluate::evaluate(...)
36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)             0L    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})        else 2L    }, output_handler = knit_handlers(options$render, options))

25: eval(call)37: in_dir(input_dir(), expr)

26: eval(call)38: 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) 
27: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE            0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
39: eng_r(options)
40: block_exec(params)
41: }, handlers)
28: doWithOneRestart(return(expr), restart)
29: call_block(x)
42: process_group(group)
43: withOneRestart(expr, restarts[[1L]])
30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr])
31: doWithOneRestart(return(expr), restart)
32:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
44: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts)
34:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    }), list(rlang_trace_top_env = knit_global()))
45:     TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 35: evaluate::evaluate(...)
            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)             0L    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())        else 2L    }, output_handler = knit_handlers(options$render, options))
    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)37: in_dir(input_dir(), expr)

46: process_file(text, output)38: 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) 
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)            0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
39: eng_r(options)    output_dir = getwd(), ...)
49: 
40: block_exec(params)vweave_rmarkdown(...)
50: 
41: call_block(x)
42: process_group(group)engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: 
43: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]])
53:         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })tryCatchList(expr, classes, parentenv, handlers)
54: 
44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
45: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...
        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
46: process_file(text, output)
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
49: vweave_rmarkdown(...)
50: engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: 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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...

Quitting from clustra_bp_vignette.Rmd:71-74 [run5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
    ▆
 1. └─clustra::clustra(...)
 2.   └─clustra::trajectories(...)
 3.     └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clustra_bp_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_bp_vignette.Rmd’

--- re-building ‘clustra_vignette.Rmd’ using rmarkdown

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

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

Traceback:
 1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit,     terms = terms, exclude = exclude, block.size = block.size,     newdata.guaranteed = newdata.guaranteed, na.action = na.action,     ...)
 2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 4: FUN(X[[i]], ...)
 5: lapply(X = S, FUN = FUN, ...)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: 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))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10,     0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: 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)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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)    })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...

Traceback:
 1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit,     terms = terms, exclude = exclude, block.size = block.size,     newdata.guaranteed = newdata.guaranteed, na.action = na.action,     ...)
 2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 4: FUN(X[[i]], ...)
 5: lapply(X = S, FUN = FUN, ...)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: 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))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10,     0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: 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)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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)    })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...

Quitting from clustra_vignette.Rmd:129-139 [hclust_d]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
    ▆
 1. └─clustra::clustra(...)
 2.   └─clustra:::start_groups(...)
 3.     └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clustra_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘clustra_bp_vignette.Rmd’ ‘clustra_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted