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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spoon
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* checking for file ‘spoon/DESCRIPTION’ ... OK
* preparing ‘spoon’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spoon.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: BRISC_estimation(coords = coords, y = y_i, x = NULL, cov.model = "exponential",     ordering = order_brisc, neighbor = nn_brisc, verbose = FALSE)
 2: system.time({    out_i <- BRISC_estimation(coords = coords, y = y_i, x = NULL,         cov.model = "exponential", ordering = order_brisc, neighbor = nn_brisc,         verbose = FALSE)})
 3: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
 4: suppressWarnings({    runtime <- system.time({        out_i <- BRISC_estimation(coords = coords, y = y_i, x = NULL,             cov.model = "exponential", ordering = order_brisc,             neighbor = nn_brisc, verbose = FALSE)    })})
 5: FUN(...)
 6: withCallingHandlers({    ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()    FUN(...)}, error = function(e) {    annotated_condition <- handle_error(e)    stop(annotated_condition)}, warning = handle_warning)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({    withCallingHandlers({        ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()        FUN(...)    }, error = function(e) {        annotated_condition <- handle_error(e)        stop(annotated_condition)    }, warning = handle_warning)}, error = identity)
11: FUN(X[[i]], ...)
12: (function (X, FUN, ...) {    FUN <- match.fun(FUN)    if (!is.vector(X) || is.object(X))         X <- as.list(X)    .Internal(lapply(X, FUN))})(X = 1:10, FUN = function (...) {    if (!identical(timeout, WORKER_TIMEOUT)) {        setTimeLimit(timeout, timeout, TRUE)        on.exit(setTimeLimit(Inf, Inf, FALSE))    }    if (!is.null(globalOptions))         base::options(globalOptions)    if (stop.on.error && ERROR_OCCURRED) {        UNEVALUATED    }    else {        .rng_reset_generator("L'Ecuyer-CMRG", SEED)        output <- tryCatch({            withCallingHandlers({                ERROR_CALL_DEPTH <<- (function() sys.nframe() -                   1L)()                FUN(...)            }, error = function(e) {                annotated_condition <- handle_error(e)                stop(annotated_condition)            }, warning = handle_warning)        }, error = identity)        if (force.GC)             gc(verbose = FALSE, full = FALSE)        SEED <<- .rng_next_substream(SEED)        output    }})
13: do.call(lapply, args)
14: BiocParallel:::.workerLapply_impl(...)
15: (function (...) BiocParallel:::.workerLapply_impl(...))(X = 1:10, FUN = function (i) {    y_i <- y[, i]    suppressWarnings({        runtime <- system.time({            out_i <- BRISC_estimation(coords = coords, y = y_i,                 x = NULL, cov.model = "exponential", ordering = order_brisc,                 neighbor = nn_brisc, verbose = FALSE)        })    })    pred_i <- BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL,         verbose = FALSE)    residual_i <- y_i - pred_i$prediction    return(c(pred_i$prediction, residual_i))}, ARGS = list(), OPTIONS = list(log = FALSE, threshold = "INFO",     stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_,     force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, 1226132466L, -421848373L, 412861328L, 1631185489L, -1231568930L, -1407128889L), GLOBALS = list(), PACKAGES = character(0))
16: do.call(msg$data$fun, msg$data$args)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({    do.call(msg$data$fun, msg$data$args)}, error = function(e) {    list(.error_worker_comm(e, "worker evaluation failed"))})
21: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
22: .recv_any(manager$backend)
23: .recv_any(manager$backend)
24: .manager_recv(manager)
25: .manager_recv(manager)
26: .collect_result(manager, reducer, progress, BPPARAM)
27: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer,     progress.length = length(redo_index))
28: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS,     ...)
29: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
30: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
31: bplapply(ix, function(i) {    y_i <- y[, i]    suppressWarnings({        runtime <- system.time({            out_i <- BRISC_estimation(coords = coords, y = y_i,                 x = NULL, cov.model = "exponential", ordering = order_brisc,                 neighbor = nn_brisc, verbose = FALSE)        })    })    pred_i <- BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL,         verbose = FALSE)    residual_i <- y_i - pred_i$prediction    return(c(pred_i$prediction, residual_i))}, BPPARAM = BPPARAM)
32: bplapply(ix, function(i) {    y_i <- y[, i]    suppressWarnings({        runtime <- system.time({            out_i <- BRISC_estimation(coords = coords, y = y_i,                 x = NULL, cov.model = "exponential", ordering = order_brisc,                 neighbor = nn_brisc, verbose = FALSE)        })    })    pred_i <- BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL,         verbose = FALSE)    residual_i <- y_i - pred_i$prediction    return(c(pred_i$prediction, residual_i))}, BPPARAM = BPPARAM)
33: generate_weights(input = spe, stabilize = TRUE, BPPARAM = MulticoreParam(workers = 1,     RNGseed = 4))
34: eval(expr, envir)
35: eval(expr, envir)
36: withVisible(eval(expr, envir))
37: withCallingHandlers(code, message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
38: eval(call)
39: eval(call)
40: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestartList(expr, restarts[-nr])
44: doWithOneRestart(return(expr), restart)
45: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
46: withRestartList(expr, restarts)
47: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
48: evaluate::evaluate(...)
49: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
50: in_dir(input_dir(), expr)
51: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
52: eng_r(options)
53: block_exec(params)
54: call_block(x)
55: process_group(group)
56: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
57: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
58: process_file(text, output)
59: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
60: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
61: vweave_rmarkdown(...)
62: engine$weave(file, quiet = quiet, encoding = enc)
63: doTryCatch(return(expr), name, parentenv, handler)
64: tryCatchOne(expr, names, parentenv, handlers[[1L]])
65: tryCatchList(expr, classes, parentenv, handlers)
66: 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)))})
67: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)